X-PLOR: V3.840 user: on: Alpha/OSF at: 18-Aug-96 02:20:42 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! refine.inp -- Clean up the output of dgsa.inp using simulated annealing, X-PLOR>! including Van der Waals and electrostatic forces X-PLOR>! Dave Schweisguth , 21 Jul 1996 X-PLOR>! Derived from nmr/refine_gentle.inp X-PLOR> X-PLOR>evaluate ($t=300) ! Temperature for constant-temperature MD EVALUATE: symbol $T set to 300.000 (real) X-PLOR>evaluate ($steps=40000) ! Number of steps of constant-temperature MD EVALUATE: symbol $STEPS set to 40000.0 (real) X-PLOR>evaluate ($timestep=0.0005) ! Time of each MD step EVALUATE: symbol $TIMESTEP set to 0.500000E-03 (real) X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use 'xplor -s' ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/xplor.seed opened. SEED=71903.5070800781 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> ctonnb=9.5 NBDSET> ctofnb=10.5 NBDSET> cutnb=11.5 NBDSET> tolerance=0.5 NBDSET> rdie NBDSET> switch NBDSET> vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR>restraints dihedral scale=800 end X-PLOR> X-PLOR>coordinates @dgsa.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb" COOR>REMARK 5 DATE:17-Aug-96 19:08:18 created by user: COOR>ATOM 1 P GUA A 1 -18.066 -1.775 -1.373 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -18.640 -0.492 -0.894 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> X-PLOR>flags exclude * include bond angl dihe impr vdw elec noe cdih plan end X-PLOR> X-PLOR>! Intial minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2090 exclusions and 1650 interactions(1-4) %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.10 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.10 A apart %atoms "A -1 -GUA -N1 " and "A -20 -CYT -H1' " only 1.45 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.41 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H5 " only 1.42 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -C4 " and "A -3 -CYT -N1 " only 1.31 A apart %atoms "A -2 -GUA -C4 " and "A -3 -CYT -C2 " only 1.16 A apart %atoms "A -2 -GUA -N3 " and "A -3 -CYT -N1 " only 0.69 A apart %atoms "A -2 -GUA -N3 " and "A -3 -CYT -C2 " only 1.33 A apart %atoms "A -2 -GUA -C6 " and "A -3 -CYT -N3 " only 1.23 A apart %atoms "A -2 -GUA -C6 " and "A -3 -CYT -C4 " only 1.23 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.21 A apart %atoms "A -2 -GUA -C5 " and "A -3 -CYT -N3 " only 0.99 A apart %atoms "A -2 -GUA -C5 " and "A -3 -CYT -C4 " only 1.17 A apart %atoms "A -2 -GUA -C5 " and "A -19 -GUA -H22 " only 1.12 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -N2 " only 1.24 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 0.79 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H22 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.34 A apart %atoms "A -3 -CYT -N3 " and "A -19 -GUA -H22 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 0.77 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.42 A apart %atoms "A -3 -CYT -H5 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -4 -ADE -N6 " and "A -20 -CYT -H42 " only 1.30 A apart %atoms "A -4 -ADE -H61 " and "A -20 -CYT -H42 " only 1.42 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -C2 " and "A -21 -CYT -H42 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -N4 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 0.56 A apart NBONDS: found 71292 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.10 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.10 A apart %atoms "A -1 -GUA -N1 " and "A -20 -CYT -H1' " only 1.45 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H5 " only 1.42 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -C1' " and "A -3 -CYT -N1 " only 1.37 A apart %atoms "A -2 -GUA -H1' " and "A -3 -CYT -N1 " only 1.50 A apart %atoms "A -2 -GUA -C4 " and "A -3 -CYT -C2 " only 1.26 A apart %atoms "A -2 -GUA -C6 " and "A -3 -CYT -N3 " only 1.25 A apart %atoms "A -2 -GUA -C6 " and "A -3 -CYT -C4 " only 1.28 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.21 A apart %atoms "A -2 -GUA -C5 " and "A -3 -CYT -N3 " only 1.43 A apart %atoms "A -2 -GUA -C5 " and "A -3 -CYT -C4 " only 1.31 A apart %atoms "A -2 -GUA -C5 " and "A -19 -GUA -H22 " only 1.16 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -N2 " only 1.27 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 0.83 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H22 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.34 A apart %atoms "A -3 -CYT -N3 " and "A -19 -GUA -H22 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 0.89 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H5 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -4 -ADE -N6 " and "A -20 -CYT -H42 " only 1.30 A apart %atoms "A -4 -ADE -H61 " and "A -20 -CYT -H42 " only 1.42 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -C2 " and "A -21 -CYT -H42 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -N4 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 0.56 A apart NBONDS: found 71293 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.13 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.13 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H5 " only 1.44 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.35 A apart %atoms "A -2 -GUA -C5 " and "A -19 -GUA -H22 " only 1.32 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.46 A apart %atoms "A -3 -CYT -H5 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -4 -ADE -N6 " and "A -20 -CYT -H42 " only 1.35 A apart %atoms "A -4 -ADE -H61 " and "A -20 -CYT -H42 " only 1.44 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -C2 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 0.75 A apart NBONDS: found 71266 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.19 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.21 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.22 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H5 " only 1.48 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.39 A apart %atoms "A -2 -GUA -N3 " and "A -3 -CYT -N1 " only 1.40 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.49 A apart %atoms "A -2 -GUA -C5 " and "A -19 -GUA -H22 " only 1.40 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.47 A apart %atoms "A -4 -ADE -N6 " and "A -20 -CYT -H42 " only 1.43 A apart %atoms "A -4 -ADE -H61 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.30 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 0.86 A apart NBONDS: found 71243 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =17935.365 grad(E)=95.364 E(BOND)=4901.661 E(ANGL)=1520.444 | | E(DIHE)=0.000 E(IMPR)=1663.540 E(VDW )=5174.678 E(ELEC)=-108.655 | | E(CDIH)=211.915 E(NOE )=4163.439 E(PLAN)=408.343 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.22 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.18 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.45 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -O5' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 1.49 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.38 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.04 A apart NBONDS: found 71132 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =16151.765 grad(E)=18.529 E(BOND)=3811.797 E(ANGL)=1486.313 | | E(DIHE)=0.000 E(IMPR)=1447.937 E(VDW )=3814.034 E(ELEC)=-101.056 | | E(CDIH)=198.322 E(NOE )=5046.333 E(PLAN)=448.085 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.21 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.18 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.22 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.37 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.49 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -O5' " and "A -3 -CYT -H6 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.42 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70963 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =15862.251 grad(E)=20.192 E(BOND)=3659.020 E(ANGL)=1434.456 | | E(DIHE)=0.000 E(IMPR)=1406.053 E(VDW )=3520.821 E(ELEC)=-101.696 | | E(CDIH)=191.716 E(NOE )=5290.451 E(PLAN)=461.430 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.23 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.18 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -C2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.20 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 70857 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.24 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.17 A apart %atoms "A -1 -GUA -H1 " and "A -3 -CYT -H41 " only 1.49 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.47 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.09 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 70768 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =15506.585 grad(E)=18.812 E(BOND)=3507.749 E(ANGL)=1327.537 | | E(DIHE)=0.000 E(IMPR)=1375.187 E(VDW )=3482.365 E(ELEC)=-116.641 | | E(CDIH)=184.833 E(NOE )=5296.176 E(PLAN)=449.379 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.27 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.18 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -O6 " and "A -3 -CYT -H42 " only 1.50 A apart %atoms "A -2 -GUA -N7 " and "A -19 -GUA -H21 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -N4 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.19 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 70796 intra-atom interactions --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =15272.869 grad(E)=15.086 E(BOND)=3442.038 E(ANGL)=1226.313 | | E(DIHE)=0.000 E(IMPR)=1287.308 E(VDW )=3554.454 E(ELEC)=-114.064 | | E(CDIH)=185.310 E(NOE )=5260.809 E(PLAN)=430.700 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =15154.113 grad(E)=7.946 E(BOND)=3439.050 E(ANGL)=1205.387 | | E(DIHE)=0.000 E(IMPR)=1358.782 E(VDW )=3570.973 E(ELEC)=-115.049 | | E(CDIH)=159.946 E(NOE )=5108.397 E(PLAN)=426.627 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.21 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70734 intra-atom interactions --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =15076.569 grad(E)=9.565 E(BOND)=3398.801 E(ANGL)=1160.906 | | E(DIHE)=0.000 E(IMPR)=1338.246 E(VDW )=3519.958 E(ELEC)=-113.241 | | E(CDIH)=141.385 E(NOE )=5203.255 E(PLAN)=427.258 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =15022.426 grad(E)=10.261 E(BOND)=3385.253 E(ANGL)=1165.875 | | E(DIHE)=0.000 E(IMPR)=1358.697 E(VDW )=3485.958 E(ELEC)=-116.063 | | E(CDIH)=134.402 E(NOE )=5183.404 E(PLAN)=424.899 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Constant temperature SA X-PLOR> X-PLOR>vector do (fbeta=100) (all) ! Coupling to heat bath. SELRPN: 677 atoms have been selected out of 677 X-PLOR>dynamics verlet DYNAmics> iasvel=maxwell DYNAmics> firsttemperature=$t DYNAmics> tbath=$t DYNAmics> tcoup=true DYNAmics> nstep=$steps DYNAmics> timestep=$timestep DYNAmics> nprint=250 DYNAmics> iprfrq=2500 DYNAmics> trajectory=refine.tra DYNAmics> nsavc=200 ! Save trajectory to file. DYNAmics>end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 0.130127202E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.04225 0.01807 -0.00737 velocity [A/ps] : -0.02112 0.11548 -0.18762 ang. mom. [amu A/ps] : -291.17871 -828.84622 4814.62475 kin. ener. [Kcal/mol] : 0.39481 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.04225 0.01807 -0.00737 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=15605.671 E(kin)=583.245 temperature=289.022 | | Etotal =15022.426 grad(E)=10.261 E(BOND)=3385.253 E(ANGL)=1165.875 | | E(DIHE)=0.000 E(IMPR)=1358.697 E(VDW )=3485.958 E(ELEC)=-116.063 | | E(CDIH)=134.402 E(NOE )=5183.404 E(PLAN)=424.899 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.41 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 70744 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.24 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -4 -ADE -H62 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70816 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.21 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 70843 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.24 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.41 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70847 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.22 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70818 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.20 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.42 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 70811 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.41 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 70734 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70572 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 70445 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=15936.306 E(kin)=633.106 temperature=313.730 | | Etotal =15303.200 grad(E)=56.014 E(BOND)=3558.928 E(ANGL)=1319.964 | | E(DIHE)=0.000 E(IMPR)=1391.227 E(VDW )=3357.577 E(ELEC)=-125.939 | | E(CDIH)=158.208 E(NOE )=5222.157 E(PLAN)=421.078 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 70299 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70185 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.40 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 70143 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70067 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 70002 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69949 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69849 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69702 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69556 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=15833.564 E(kin)=585.793 temperature=290.285 | | Etotal =15247.771 grad(E)=56.664 E(BOND)=3483.589 E(ANGL)=1273.749 | | E(DIHE)=0.000 E(IMPR)=1375.158 E(VDW )=3351.659 E(ELEC)=-138.070 | | E(CDIH)=222.269 E(NOE )=5273.735 E(PLAN)=405.682 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.41 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69457 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69445 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69421 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69380 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69369 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69307 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69214 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69152 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.38 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69064 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69042 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=15902.437 E(kin)=604.194 temperature=299.404 | | Etotal =15298.243 grad(E)=55.027 E(BOND)=3542.925 E(ANGL)=1278.472 | | E(DIHE)=0.000 E(IMPR)=1417.437 E(VDW )=3264.496 E(ELEC)=-148.483 | | E(CDIH)=223.528 E(NOE )=5325.820 E(PLAN)=394.047 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68969 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68891 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68866 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.41 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.19 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68845 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68815 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.41 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68755 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.44 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H22 " and "A -3 -CYT -N4 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.17 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68740 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68749 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.17 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68748 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68795 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68802 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68838 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=15959.940 E(kin)=594.032 temperature=294.368 | | Etotal =15365.908 grad(E)=60.359 E(BOND)=3569.083 E(ANGL)=1341.441 | | E(DIHE)=0.000 E(IMPR)=1421.613 E(VDW )=3293.954 E(ELEC)=-143.742 | | E(CDIH)=180.321 E(NOE )=5317.771 E(PLAN)=385.467 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68894 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69012 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69074 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69187 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69225 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69298 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69357 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69526 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69668 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69733 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69779 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69814 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69843 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=15962.234 E(kin)=605.961 temperature=300.279 | | Etotal =15356.272 grad(E)=57.469 E(BOND)=3562.157 E(ANGL)=1322.390 | | E(DIHE)=0.000 E(IMPR)=1463.697 E(VDW )=3330.633 E(ELEC)=-135.206 | | E(CDIH)=178.413 E(NOE )=5234.586 E(PLAN)=399.602 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69825 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69799 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69729 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69708 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69729 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69715 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69706 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.18 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69706 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69708 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69786 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69815 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69838 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=15882.692 E(kin)=615.172 temperature=304.844 | | Etotal =15267.519 grad(E)=57.777 E(BOND)=3571.162 E(ANGL)=1277.493 | | E(DIHE)=0.000 E(IMPR)=1431.985 E(VDW )=3307.661 E(ELEC)=-136.978 | | E(CDIH)=206.608 E(NOE )=5195.659 E(PLAN)=413.930 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69878 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69831 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69838 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69857 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69913 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69959 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70004 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.42 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70071 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.44 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70149 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.40 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70215 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=15925.120 E(kin)=617.225 temperature=305.861 | | Etotal =15307.894 grad(E)=55.958 E(BOND)=3519.287 E(ANGL)=1268.466 | | E(DIHE)=0.000 E(IMPR)=1449.873 E(VDW )=3410.566 E(ELEC)=-131.954 | | E(CDIH)=242.069 E(NOE )=5131.233 E(PLAN)=418.354 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H5T " and "A -20 -CYT -H4' " only 1.46 A apart %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.43 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70269 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70245 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 70245 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70198 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 70119 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70068 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69983 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69968 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69877 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69880 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69862 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=15889.643 E(kin)=614.795 temperature=304.657 | | Etotal =15274.848 grad(E)=57.101 E(BOND)=3508.593 E(ANGL)=1296.903 | | E(DIHE)=0.000 E(IMPR)=1417.407 E(VDW )=3381.684 E(ELEC)=-129.008 | | E(CDIH)=180.122 E(NOE )=5200.623 E(PLAN)=418.523 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69824 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69767 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H3' " only 1.43 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69755 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69668 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69652 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69656 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.44 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69663 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.43 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69698 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.42 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69721 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.41 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69747 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H3' " only 1.45 A apart %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.45 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69764 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69809 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69850 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69800 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69810 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69810 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=15908.618 E(kin)=615.200 temperature=304.858 | | Etotal =15293.418 grad(E)=58.906 E(BOND)=3513.486 E(ANGL)=1346.174 | | E(DIHE)=0.000 E(IMPR)=1416.071 E(VDW )=3347.516 E(ELEC)=-132.322 | | E(CDIH)=171.066 E(NOE )=5214.548 E(PLAN)=416.880 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69794 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H3' " only 1.34 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69762 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69724 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69757 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69698 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69605 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69433 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69287 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69158 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68979 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68831 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68750 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=15933.693 E(kin)=594.422 temperature=294.561 | | Etotal =15339.271 grad(E)=60.423 E(BOND)=3562.330 E(ANGL)=1297.334 | | E(DIHE)=0.000 E(IMPR)=1414.262 E(VDW )=3339.708 E(ELEC)=-124.643 | | E(CDIH)=206.140 E(NOE )=5224.439 E(PLAN)=419.701 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15924.629 E(kin)=604.265 temperature=299.438 | | Etotal =15320.364 grad(E)=58.657 E(BOND)=3548.428 E(ANGL)=1309.411 | | E(DIHE)=0.000 E(IMPR)=1413.097 E(VDW )=3335.685 E(ELEC)=-135.679 | | E(CDIH)=197.192 E(NOE )=5244.487 E(PLAN)=407.743 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=53.227 E(kin)=20.837 temperature=10.326 | | Etotal =53.236 grad(E)=1.944 E(BOND)=37.177 E(ANGL)=33.368 | | E(DIHE)=0.000 E(IMPR)=32.052 E(VDW )=67.514 E(ELEC)=8.762 | | E(CDIH)=22.728 E(NOE )=53.243 E(PLAN)=11.211 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68665 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68638 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -20 -CYT -H4' " only 1.42 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68578 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68524 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68459 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68361 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68244 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 68063 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 67851 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 67741 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=15965.097 E(kin)=593.334 temperature=294.022 | | Etotal =15371.763 grad(E)=62.300 E(BOND)=3526.725 E(ANGL)=1303.952 | | E(DIHE)=0.000 E(IMPR)=1396.764 E(VDW )=3403.501 E(ELEC)=-127.328 | | E(CDIH)=192.364 E(NOE )=5258.435 E(PLAN)=417.350 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 67598 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 67550 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67614 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67687 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 67699 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67683 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67619 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=15875.570 E(kin)=617.624 temperature=306.058 | | Etotal =15257.946 grad(E)=59.388 E(BOND)=3473.809 E(ANGL)=1294.694 | | E(DIHE)=0.000 E(IMPR)=1444.565 E(VDW )=3336.235 E(ELEC)=-139.464 | | E(CDIH)=194.608 E(NOE )=5242.056 E(PLAN)=411.443 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67579 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67519 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67540 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67535 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67546 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 67595 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.39 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67653 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 67691 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67723 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 67785 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=15882.841 E(kin)=611.659 temperature=303.103 | | Etotal =15271.182 grad(E)=58.164 E(BOND)=3484.466 E(ANGL)=1317.320 | | E(DIHE)=0.000 E(IMPR)=1392.606 E(VDW )=3368.849 E(ELEC)=-131.786 | | E(CDIH)=188.785 E(NOE )=5239.983 E(PLAN)=410.959 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67908 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68084 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68188 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68326 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68462 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68581 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68669 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68786 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=15924.074 E(kin)=614.108 temperature=304.316 | | Etotal =15309.966 grad(E)=59.426 E(BOND)=3504.689 E(ANGL)=1339.180 | | E(DIHE)=0.000 E(IMPR)=1374.999 E(VDW )=3381.613 E(ELEC)=-123.500 | | E(CDIH)=209.517 E(NOE )=5212.583 E(PLAN)=410.884 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68847 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.40 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68886 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68926 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69006 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69028 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69014 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68991 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69039 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69058 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69046 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=15964.800 E(kin)=601.564 temperature=298.100 | | Etotal =15363.236 grad(E)=62.069 E(BOND)=3611.428 E(ANGL)=1307.620 | | E(DIHE)=0.000 E(IMPR)=1387.354 E(VDW )=3272.438 E(ELEC)=-124.216 | | E(CDIH)=230.886 E(NOE )=5267.208 E(PLAN)=410.518 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69084 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69088 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69132 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69212 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69239 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69272 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69332 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69395 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69428 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69461 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69475 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69527 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69514 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=15927.530 E(kin)=599.440 temperature=297.047 | | Etotal =15328.090 grad(E)=63.156 E(BOND)=3547.103 E(ANGL)=1306.150 | | E(DIHE)=0.000 E(IMPR)=1424.028 E(VDW )=3319.192 E(ELEC)=-132.718 | | E(CDIH)=198.368 E(NOE )=5255.065 E(PLAN)=410.903 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69472 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69479 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69438 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69426 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H4' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69312 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69252 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.46 A apart NBONDS: found 69273 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69272 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69281 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69278 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.27 A apart NBONDS: found 69259 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=15908.882 E(kin)=605.829 temperature=300.214 | | Etotal =15303.053 grad(E)=60.515 E(BOND)=3557.992 E(ANGL)=1333.888 | | E(DIHE)=0.000 E(IMPR)=1423.509 E(VDW )=3289.669 E(ELEC)=-137.209 | | E(CDIH)=213.052 E(NOE )=5225.952 E(PLAN)=396.201 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69272 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69280 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69247 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69167 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69109 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69099 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68991 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69034 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69007 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=15945.806 E(kin)=605.258 temperature=299.931 | | Etotal =15340.548 grad(E)=61.448 E(BOND)=3606.045 E(ANGL)=1350.270 | | E(DIHE)=0.000 E(IMPR)=1356.364 E(VDW )=3337.074 E(ELEC)=-127.194 | | E(CDIH)=185.381 E(NOE )=5221.698 E(PLAN)=410.909 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69007 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69017 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69050 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69043 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69090 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69142 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69179 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69185 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.39 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69249 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=15962.590 E(kin)=582.351 temperature=288.579 | | Etotal =15380.239 grad(E)=65.037 E(BOND)=3577.300 E(ANGL)=1370.767 | | E(DIHE)=0.000 E(IMPR)=1481.087 E(VDW )=3280.968 E(ELEC)=-138.482 | | E(CDIH)=206.564 E(NOE )=5180.066 E(PLAN)=421.969 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69195 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69242 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69169 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69111 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69028 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68969 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68791 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68707 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=15975.734 E(kin)=625.134 temperature=309.780 | | Etotal =15350.600 grad(E)=61.713 E(BOND)=3552.004 E(ANGL)=1303.529 | | E(DIHE)=0.000 E(IMPR)=1410.146 E(VDW )=3302.670 E(ELEC)=-138.273 | | E(CDIH)=190.153 E(NOE )=5312.270 E(PLAN)=418.100 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15937.722 E(kin)=605.315 temperature=299.959 | | Etotal =15332.406 grad(E)=60.768 E(BOND)=3552.608 E(ANGL)=1320.296 | | E(DIHE)=0.000 E(IMPR)=1412.236 E(VDW )=3342.361 E(ELEC)=-131.909 | | E(CDIH)=201.570 E(NOE )=5224.912 E(PLAN)=410.333 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=26.904 E(kin)=11.452 temperature=5.675 | | Etotal =29.104 grad(E)=1.538 E(BOND)=36.276 E(ANGL)=26.273 | | E(DIHE)=0.000 E(IMPR)=27.035 E(VDW )=48.476 E(ELEC)=5.557 | | E(CDIH)=15.610 E(NOE )=41.685 E(PLAN)=6.815 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=15931.175 E(kin)=604.790 temperature=299.699 | | Etotal =15326.385 grad(E)=59.713 E(BOND)=3550.518 E(ANGL)=1314.853 | | E(DIHE)=0.000 E(IMPR)=1412.666 E(VDW )=3339.023 E(ELEC)=-133.794 | | E(CDIH)=199.381 E(NOE )=5234.700 E(PLAN)=409.038 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=42.677 E(kin)=16.821 temperature=8.335 | | Etotal =43.322 grad(E)=2.046 E(BOND)=36.789 E(ANGL)=30.520 | | E(DIHE)=0.000 E(IMPR)=29.653 E(VDW )=58.866 E(ELEC)=7.575 | | E(CDIH)=19.619 E(NOE )=48.806 E(PLAN)=9.367 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68620 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68542 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68473 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68462 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68439 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68408 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68417 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68360 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=15961.535 E(kin)=594.563 temperature=294.631 | | Etotal =15366.972 grad(E)=62.468 E(BOND)=3550.692 E(ANGL)=1368.547 | | E(DIHE)=0.000 E(IMPR)=1382.390 E(VDW )=3372.069 E(ELEC)=-127.311 | | E(CDIH)=184.355 E(NOE )=5219.152 E(PLAN)=417.078 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68334 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68310 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68279 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68197 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68161 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68145 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68065 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68028 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68005 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=15969.108 E(kin)=625.402 temperature=309.913 | | Etotal =15343.705 grad(E)=61.258 E(BOND)=3572.471 E(ANGL)=1327.971 | | E(DIHE)=0.000 E(IMPR)=1450.113 E(VDW )=3335.239 E(ELEC)=-128.576 | | E(CDIH)=164.538 E(NOE )=5223.040 E(PLAN)=398.910 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67938 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.48 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67900 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67870 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67851 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67819 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.39 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67781 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67791 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 67743 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67691 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67681 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67656 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 67619 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67635 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67627 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 67603 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=15927.312 E(kin)=624.738 temperature=309.584 | | Etotal =15302.573 grad(E)=59.535 E(BOND)=3558.847 E(ANGL)=1283.820 | | E(DIHE)=0.000 E(IMPR)=1418.122 E(VDW )=3311.810 E(ELEC)=-142.424 | | E(CDIH)=198.566 E(NOE )=5260.825 E(PLAN)=413.007 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 67623 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67650 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 67686 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 67748 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 67890 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68002 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68034 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68114 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68162 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=15968.619 E(kin)=596.516 temperature=295.599 | | Etotal =15372.103 grad(E)=63.343 E(BOND)=3639.156 E(ANGL)=1331.535 | | E(DIHE)=0.000 E(IMPR)=1418.636 E(VDW )=3286.679 E(ELEC)=-143.582 | | E(CDIH)=203.013 E(NOE )=5232.712 E(PLAN)=403.954 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68204 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68198 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68218 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68197 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68193 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 68161 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68155 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68151 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68108 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68137 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68114 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68172 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=15914.394 E(kin)=611.143 temperature=302.847 | | Etotal =15303.251 grad(E)=60.069 E(BOND)=3557.060 E(ANGL)=1348.495 | | E(DIHE)=0.000 E(IMPR)=1383.444 E(VDW )=3251.603 E(ELEC)=-121.838 | | E(CDIH)=210.699 E(NOE )=5266.482 E(PLAN)=407.308 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68133 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68191 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68247 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68321 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68347 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68441 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68567 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68699 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68789 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 68872 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68888 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=15963.756 E(kin)=597.595 temperature=296.134 | | Etotal =15366.160 grad(E)=62.382 E(BOND)=3573.237 E(ANGL)=1317.477 | | E(DIHE)=0.000 E(IMPR)=1381.727 E(VDW )=3336.464 E(ELEC)=-131.149 | | E(CDIH)=193.979 E(NOE )=5289.516 E(PLAN)=404.908 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68879 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68913 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68903 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68863 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68879 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68902 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68936 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68952 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68933 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68923 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68894 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68850 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=15958.622 E(kin)=604.515 temperature=299.563 | | Etotal =15354.107 grad(E)=62.112 E(BOND)=3615.859 E(ANGL)=1325.273 | | E(DIHE)=0.000 E(IMPR)=1439.610 E(VDW )=3263.691 E(ELEC)=-120.652 | | E(CDIH)=192.378 E(NOE )=5230.317 E(PLAN)=407.631 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68801 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.40 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68771 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68738 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68685 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68624 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.41 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68529 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68475 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68430 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68393 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68407 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68385 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=15952.626 E(kin)=606.508 temperature=300.550 | | Etotal =15346.118 grad(E)=64.598 E(BOND)=3534.876 E(ANGL)=1344.583 | | E(DIHE)=0.000 E(IMPR)=1424.993 E(VDW )=3353.384 E(ELEC)=-135.489 | | E(CDIH)=196.147 E(NOE )=5219.547 E(PLAN)=408.077 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.44 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68366 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68433 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68421 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68395 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68356 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68230 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68209 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68084 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68034 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67957 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67909 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67842 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=15923.809 E(kin)=601.808 temperature=298.221 | | Etotal =15322.001 grad(E)=63.568 E(BOND)=3559.670 E(ANGL)=1321.127 | | E(DIHE)=0.000 E(IMPR)=1431.806 E(VDW )=3326.524 E(ELEC)=-140.091 | | E(CDIH)=210.910 E(NOE )=5203.909 E(PLAN)=408.145 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67792 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 67692 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67609 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67516 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67536 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67473 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67512 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 67552 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67567 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=15945.135 E(kin)=594.678 temperature=294.688 | | Etotal =15350.457 grad(E)=64.013 E(BOND)=3591.400 E(ANGL)=1342.919 | | E(DIHE)=0.000 E(IMPR)=1443.734 E(VDW )=3268.168 E(ELEC)=-130.531 | | E(CDIH)=172.977 E(NOE )=5252.471 E(PLAN)=409.319 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15949.175 E(kin)=605.559 temperature=300.080 | | Etotal =15343.616 grad(E)=62.609 E(BOND)=3562.903 E(ANGL)=1323.945 | | E(DIHE)=0.000 E(IMPR)=1418.519 E(VDW )=3340.364 E(ELEC)=-132.822 | | E(CDIH)=194.196 E(NOE )=5227.205 E(PLAN)=409.306 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=20.216 E(kin)=11.704 temperature=5.800 | | Etotal =22.970 grad(E)=1.422 E(BOND)=38.855 E(ANGL)=26.275 | | E(DIHE)=0.000 E(IMPR)=25.891 E(VDW )=47.699 E(ELEC)=6.974 | | E(CDIH)=14.274 E(NOE )=39.266 E(PLAN)=4.567 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=15937.175 E(kin)=605.046 temperature=299.826 | | Etotal =15332.129 grad(E)=60.678 E(BOND)=3554.646 E(ANGL)=1317.884 | | E(DIHE)=0.000 E(IMPR)=1414.617 E(VDW )=3339.470 E(ELEC)=-133.470 | | E(CDIH)=197.652 E(NOE )=5232.202 E(PLAN)=409.127 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=37.715 E(kin)=15.311 temperature=7.587 | | Etotal =38.640 grad(E)=2.308 E(BOND)=37.942 E(ANGL)=29.487 | | E(DIHE)=0.000 E(IMPR)=28.588 E(VDW )=55.398 E(ELEC)=7.394 | | E(CDIH)=18.180 E(NOE )=45.983 E(PLAN)=8.091 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67569 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.19 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.27 A apart NBONDS: found 67584 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67495 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67473 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67544 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 67634 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67770 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67961 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68096 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=15945.120 E(kin)=620.668 temperature=307.567 | | Etotal =15324.452 grad(E)=64.349 E(BOND)=3490.740 E(ANGL)=1327.264 | | E(DIHE)=0.000 E(IMPR)=1425.614 E(VDW )=3363.517 E(ELEC)=-139.992 | | E(CDIH)=189.201 E(NOE )=5247.292 E(PLAN)=420.817 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68277 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68392 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68524 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68589 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68613 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68669 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=15949.633 E(kin)=601.247 temperature=297.943 | | Etotal =15348.386 grad(E)=62.624 E(BOND)=3563.159 E(ANGL)=1363.444 | | E(DIHE)=0.000 E(IMPR)=1437.046 E(VDW )=3352.358 E(ELEC)=-136.673 | | E(CDIH)=209.290 E(NOE )=5142.619 E(PLAN)=417.142 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68769 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68836 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68962 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69078 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69219 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69244 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69217 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69192 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=15950.729 E(kin)=608.080 temperature=301.329 | | Etotal =15342.649 grad(E)=63.444 E(BOND)=3612.467 E(ANGL)=1331.918 | | E(DIHE)=0.000 E(IMPR)=1395.493 E(VDW )=3268.523 E(ELEC)=-139.731 | | E(CDIH)=205.114 E(NOE )=5254.258 E(PLAN)=414.607 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69385 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69448 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69544 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69551 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69468 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69452 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69463 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=15953.524 E(kin)=611.863 temperature=303.204 | | Etotal =15341.661 grad(E)=63.811 E(BOND)=3569.865 E(ANGL)=1320.850 | | E(DIHE)=0.000 E(IMPR)=1459.258 E(VDW )=3317.728 E(ELEC)=-149.631 | | E(CDIH)=180.720 E(NOE )=5243.547 E(PLAN)=399.324 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69519 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69568 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69614 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69608 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69680 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69609 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69625 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=15962.316 E(kin)=590.989 temperature=292.860 | | Etotal =15371.327 grad(E)=65.707 E(BOND)=3545.597 E(ANGL)=1355.413 | | E(DIHE)=0.000 E(IMPR)=1418.518 E(VDW )=3344.799 E(ELEC)=-136.717 | | E(CDIH)=172.235 E(NOE )=5254.192 E(PLAN)=417.289 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69649 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69724 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69763 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69783 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69788 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69821 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69832 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69777 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=15955.606 E(kin)=609.799 temperature=302.181 | | Etotal =15345.807 grad(E)=66.132 E(BOND)=3575.078 E(ANGL)=1309.927 | | E(DIHE)=0.000 E(IMPR)=1417.631 E(VDW )=3393.179 E(ELEC)=-147.478 | | E(CDIH)=204.699 E(NOE )=5175.446 E(PLAN)=417.324 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.40 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69602 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69482 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69394 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69303 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69223 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69178 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69132 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=15962.804 E(kin)=614.873 temperature=304.695 | | Etotal =15347.931 grad(E)=65.309 E(BOND)=3589.022 E(ANGL)=1364.486 | | E(DIHE)=0.000 E(IMPR)=1464.983 E(VDW )=3304.766 E(ELEC)=-147.377 | | E(CDIH)=190.768 E(NOE )=5174.504 E(PLAN)=406.779 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69075 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69002 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69018 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69047 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.17 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 69069 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69027 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68868 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=15904.154 E(kin)=630.531 temperature=312.454 | | Etotal =15273.623 grad(E)=62.366 E(BOND)=3524.551 E(ANGL)=1322.574 | | E(DIHE)=0.000 E(IMPR)=1416.512 E(VDW )=3352.013 E(ELEC)=-144.225 | | E(CDIH)=208.202 E(NOE )=5184.630 E(PLAN)=409.366 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68671 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68548 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 68450 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68480 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68580 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68660 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=15931.187 E(kin)=599.072 temperature=296.865 | | Etotal =15332.116 grad(E)=65.693 E(BOND)=3605.592 E(ANGL)=1333.574 | | E(DIHE)=0.000 E(IMPR)=1441.052 E(VDW )=3348.853 E(ELEC)=-148.443 | | E(CDIH)=177.161 E(NOE )=5165.889 E(PLAN)=408.438 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68677 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68691 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68629 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68606 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68596 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68623 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68666 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=15923.036 E(kin)=614.218 temperature=304.371 | | Etotal =15308.818 grad(E)=63.467 E(BOND)=3599.368 E(ANGL)=1325.282 | | E(DIHE)=0.000 E(IMPR)=1388.585 E(VDW )=3335.634 E(ELEC)=-131.845 | | E(CDIH)=191.567 E(NOE )=5186.778 E(PLAN)=413.449 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15941.780 E(kin)=605.547 temperature=300.074 | | Etotal =15336.233 grad(E)=63.706 E(BOND)=3563.915 E(ANGL)=1329.943 | | E(DIHE)=0.000 E(IMPR)=1423.135 E(VDW )=3342.527 E(ELEC)=-142.420 | | E(CDIH)=196.947 E(NOE )=5212.473 E(PLAN)=409.713 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=15.231 E(kin)=11.028 temperature=5.465 | | Etotal =18.523 grad(E)=1.316 E(BOND)=36.760 E(ANGL)=23.098 | | E(DIHE)=0.000 E(IMPR)=25.433 E(VDW )=46.845 E(ELEC)=5.559 | | E(CDIH)=15.632 E(NOE )=40.868 E(PLAN)=5.036 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=15938.326 E(kin)=605.172 temperature=299.888 | | Etotal =15333.155 grad(E)=61.435 E(BOND)=3556.963 E(ANGL)=1320.899 | | E(DIHE)=0.000 E(IMPR)=1416.747 E(VDW )=3340.234 E(ELEC)=-135.707 | | E(CDIH)=197.476 E(NOE )=5227.269 E(PLAN)=409.274 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=33.598 E(kin)=14.362 temperature=7.117 | | Etotal =34.767 grad(E)=2.480 E(BOND)=37.863 E(ANGL)=28.509 | | E(DIHE)=0.000 E(IMPR)=28.076 E(VDW )=53.405 E(ELEC)=7.985 | | E(CDIH)=17.580 E(NOE )=45.567 E(PLAN)=7.450 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68539 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68476 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68457 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68352 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68335 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68286 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.44 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68286 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.43 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68286 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=15944.996 E(kin)=596.054 temperature=295.370 | | Etotal =15348.942 grad(E)=65.171 E(BOND)=3579.510 E(ANGL)=1312.444 | | E(DIHE)=0.000 E(IMPR)=1443.023 E(VDW )=3326.356 E(ELEC)=-139.431 | | E(CDIH)=193.405 E(NOE )=5217.411 E(PLAN)=416.226 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.48 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68273 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68233 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68046 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67989 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 67925 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67863 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 67783 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67693 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=15977.711 E(kin)=598.334 temperature=296.500 | | Etotal =15379.377 grad(E)=65.784 E(BOND)=3600.078 E(ANGL)=1326.284 | | E(DIHE)=0.000 E(IMPR)=1448.133 E(VDW )=3343.587 E(ELEC)=-134.900 | | E(CDIH)=200.934 E(NOE )=5185.489 E(PLAN)=409.772 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67672 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67596 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67471 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67339 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67311 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 67227 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67155 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=15960.111 E(kin)=595.233 temperature=294.963 | | Etotal =15364.878 grad(E)=68.239 E(BOND)=3541.877 E(ANGL)=1321.826 | | E(DIHE)=0.000 E(IMPR)=1429.436 E(VDW )=3399.008 E(ELEC)=-147.313 | | E(CDIH)=205.559 E(NOE )=5199.788 E(PLAN)=414.697 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67092 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67088 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67174 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67314 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67393 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 67408 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67369 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67322 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=15948.818 E(kin)=602.130 temperature=298.381 | | Etotal =15346.687 grad(E)=65.614 E(BOND)=3581.619 E(ANGL)=1333.979 | | E(DIHE)=0.000 E(IMPR)=1463.360 E(VDW )=3319.851 E(ELEC)=-139.353 | | E(CDIH)=173.178 E(NOE )=5209.203 E(PLAN)=404.851 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 67251 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 67281 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 67283 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67267 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 67270 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 67355 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67430 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67497 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=15944.741 E(kin)=593.658 temperature=294.183 | | Etotal =15351.083 grad(E)=68.816 E(BOND)=3578.256 E(ANGL)=1356.751 | | E(DIHE)=0.000 E(IMPR)=1406.129 E(VDW )=3294.468 E(ELEC)=-139.289 | | E(CDIH)=226.088 E(NOE )=5217.388 E(PLAN)=411.291 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67541 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 67703 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.46 A apart NBONDS: found 67984 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68258 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.19 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68378 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68513 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=15939.856 E(kin)=602.699 temperature=298.663 | | Etotal =15337.157 grad(E)=65.491 E(BOND)=3530.029 E(ANGL)=1295.000 | | E(DIHE)=0.000 E(IMPR)=1401.237 E(VDW )=3392.796 E(ELEC)=-137.669 | | E(CDIH)=223.215 E(NOE )=5225.239 E(PLAN)=407.311 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68686 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68842 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69054 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69158 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69208 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69235 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69235 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69299 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=15940.622 E(kin)=580.516 temperature=287.670 | | Etotal =15360.106 grad(E)=65.559 E(BOND)=3535.608 E(ANGL)=1325.233 | | E(DIHE)=0.000 E(IMPR)=1424.244 E(VDW )=3429.181 E(ELEC)=-139.260 | | E(CDIH)=207.780 E(NOE )=5163.887 E(PLAN)=413.433 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69381 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69474 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69547 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69530 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.19 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69485 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69480 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=15925.861 E(kin)=582.268 temperature=288.538 | | Etotal =15343.593 grad(E)=66.622 E(BOND)=3567.744 E(ANGL)=1377.803 | | E(DIHE)=0.000 E(IMPR)=1411.086 E(VDW )=3260.301 E(ELEC)=-141.476 | | E(CDIH)=183.865 E(NOE )=5280.775 E(PLAN)=403.494 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69442 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69304 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69163 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69076 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69012 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68930 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=15928.528 E(kin)=585.672 temperature=290.225 | | Etotal =15342.855 grad(E)=66.486 E(BOND)=3537.024 E(ANGL)=1344.912 | | E(DIHE)=0.000 E(IMPR)=1377.048 E(VDW )=3344.482 E(ELEC)=-130.219 | | E(CDIH)=186.713 E(NOE )=5269.922 E(PLAN)=412.972 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68993 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69064 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69061 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69075 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69095 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69055 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69081 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=15953.949 E(kin)=605.201 temperature=299.902 | | Etotal =15348.748 grad(E)=66.189 E(BOND)=3577.604 E(ANGL)=1323.426 | | E(DIHE)=0.000 E(IMPR)=1457.820 E(VDW )=3382.084 E(ELEC)=-137.259 | | E(CDIH)=204.845 E(NOE )=5123.772 E(PLAN)=416.456 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15942.686 E(kin)=605.349 temperature=299.976 | | Etotal =15337.336 grad(E)=64.793 E(BOND)=3563.699 E(ANGL)=1325.604 | | E(DIHE)=0.000 E(IMPR)=1425.252 E(VDW )=3344.135 E(ELEC)=-138.392 | | E(CDIH)=198.886 E(NOE )=5207.276 E(PLAN)=410.877 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=17.129 E(kin)=11.714 temperature=5.805 | | Etotal =20.382 grad(E)=1.456 E(BOND)=37.294 E(ANGL)=25.199 | | E(DIHE)=0.000 E(IMPR)=26.191 E(VDW )=40.273 E(ELEC)=4.289 | | E(CDIH)=14.782 E(NOE )=38.858 E(PLAN)=4.455 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=15939.198 E(kin)=605.207 temperature=299.906 | | Etotal =15333.991 grad(E)=62.107 E(BOND)=3558.311 E(ANGL)=1321.840 | | E(DIHE)=0.000 E(IMPR)=1418.448 E(VDW )=3341.014 E(ELEC)=-136.244 | | E(CDIH)=197.758 E(NOE )=5223.271 E(PLAN)=409.594 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=31.061 E(kin)=13.873 temperature=6.875 | | Etotal =32.448 grad(E)=2.673 E(BOND)=37.846 E(ANGL)=27.942 | | E(DIHE)=0.000 E(IMPR)=27.917 E(VDW )=51.073 E(ELEC)=7.472 | | E(CDIH)=17.067 E(NOE )=45.022 E(PLAN)=6.984 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69061 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69071 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69055 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69019 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68948 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68996 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=15949.766 E(kin)=614.590 temperature=304.555 | | Etotal =15335.176 grad(E)=64.837 E(BOND)=3527.092 E(ANGL)=1288.456 | | E(DIHE)=0.000 E(IMPR)=1434.469 E(VDW )=3401.337 E(ELEC)=-138.499 | | E(CDIH)=201.311 E(NOE )=5207.802 E(PLAN)=413.207 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68974 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68937 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68861 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68844 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68758 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=15963.200 E(kin)=593.318 temperature=294.014 | | Etotal =15369.882 grad(E)=65.497 E(BOND)=3570.220 E(ANGL)=1290.361 | | E(DIHE)=0.000 E(IMPR)=1444.478 E(VDW )=3373.713 E(ELEC)=-139.224 | | E(CDIH)=184.694 E(NOE )=5232.574 E(PLAN)=413.067 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68772 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68788 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68791 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68748 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68858 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68925 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=15932.590 E(kin)=617.205 temperature=305.851 | | Etotal =15315.384 grad(E)=65.756 E(BOND)=3561.608 E(ANGL)=1283.175 | | E(DIHE)=0.000 E(IMPR)=1419.048 E(VDW )=3299.862 E(ELEC)=-147.566 | | E(CDIH)=191.188 E(NOE )=5296.654 E(PLAN)=411.414 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68987 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69034 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68985 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 68854 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68928 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69083 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=15946.909 E(kin)=599.294 temperature=296.975 | | Etotal =15347.615 grad(E)=64.776 E(BOND)=3572.074 E(ANGL)=1354.211 | | E(DIHE)=0.000 E(IMPR)=1414.038 E(VDW )=3321.867 E(ELEC)=-143.375 | | E(CDIH)=206.679 E(NOE )=5220.894 E(PLAN)=401.225 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69411 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69587 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69681 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69780 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69802 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69805 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=15939.524 E(kin)=596.965 temperature=295.821 | | Etotal =15342.559 grad(E)=67.646 E(BOND)=3552.869 E(ANGL)=1371.552 | | E(DIHE)=0.000 E(IMPR)=1438.047 E(VDW )=3292.123 E(ELEC)=-144.775 | | E(CDIH)=199.120 E(NOE )=5224.995 E(PLAN)=408.629 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69759 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69684 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69658 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69672 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69651 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69647 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69522 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=15966.104 E(kin)=600.745 temperature=297.694 | | Etotal =15365.359 grad(E)=67.523 E(BOND)=3556.629 E(ANGL)=1388.928 | | E(DIHE)=0.000 E(IMPR)=1419.361 E(VDW )=3354.047 E(ELEC)=-134.452 | | E(CDIH)=182.135 E(NOE )=5187.929 E(PLAN)=410.783 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69394 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69388 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69384 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69410 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69438 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69473 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69510 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69510 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69572 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=15961.774 E(kin)=618.658 temperature=306.571 | | Etotal =15343.116 grad(E)=66.759 E(BOND)=3525.083 E(ANGL)=1351.854 | | E(DIHE)=0.000 E(IMPR)=1410.570 E(VDW )=3372.264 E(ELEC)=-138.567 | | E(CDIH)=190.049 E(NOE )=5219.334 E(PLAN)=412.529 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69618 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69671 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 69647 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69604 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69519 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69443 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69407 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69364 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=15948.741 E(kin)=615.178 temperature=304.846 | | Etotal =15333.563 grad(E)=65.647 E(BOND)=3567.620 E(ANGL)=1297.688 | | E(DIHE)=0.000 E(IMPR)=1398.782 E(VDW )=3351.260 E(ELEC)=-141.089 | | E(CDIH)=221.868 E(NOE )=5229.239 E(PLAN)=408.196 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69347 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69303 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69299 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69359 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69409 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69411 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69442 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69417 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=15940.873 E(kin)=581.694 temperature=288.254 | | Etotal =15359.178 grad(E)=65.478 E(BOND)=3605.582 E(ANGL)=1277.843 | | E(DIHE)=0.000 E(IMPR)=1402.972 E(VDW )=3301.014 E(ELEC)=-136.104 | | E(CDIH)=210.852 E(NOE )=5295.316 E(PLAN)=401.704 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69315 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69207 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69240 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69144 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69169 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69158 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69163 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=15926.637 E(kin)=607.900 temperature=301.240 | | Etotal =15318.738 grad(E)=66.045 E(BOND)=3617.630 E(ANGL)=1365.165 | | E(DIHE)=0.000 E(IMPR)=1412.220 E(VDW )=3275.441 E(ELEC)=-145.203 | | E(CDIH)=205.922 E(NOE )=5178.029 E(PLAN)=409.533 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15948.442 E(kin)=605.585 temperature=300.093 | | Etotal =15342.857 grad(E)=65.881 E(BOND)=3572.794 E(ANGL)=1332.132 | | E(DIHE)=0.000 E(IMPR)=1423.359 E(VDW )=3339.589 E(ELEC)=-141.527 | | E(CDIH)=199.393 E(NOE )=5207.282 E(PLAN)=409.836 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.704 E(kin)=12.303 temperature=6.097 | | Etotal =17.336 grad(E)=1.385 E(BOND)=34.992 E(ANGL)=25.074 | | E(DIHE)=0.000 E(IMPR)=25.270 E(VDW )=36.273 E(ELEC)=3.991 | | E(CDIH)=14.713 E(NOE )=36.643 E(PLAN)=4.529 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=15940.739 E(kin)=605.270 temperature=299.937 | | Etotal =15335.469 grad(E)=62.736 E(BOND)=3560.724 E(ANGL)=1323.555 | | E(DIHE)=0.000 E(IMPR)=1419.266 E(VDW )=3340.777 E(ELEC)=-137.125 | | E(CDIH)=198.030 E(NOE )=5220.606 E(PLAN)=409.635 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=29.030 E(kin)=13.625 temperature=6.752 | | Etotal =30.633 grad(E)=2.873 E(BOND)=37.773 E(ANGL)=27.751 | | E(DIHE)=0.000 E(IMPR)=27.555 E(VDW )=48.921 E(ELEC)=7.284 | | E(CDIH)=16.709 E(NOE )=44.141 E(PLAN)=6.639 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69145 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69111 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69069 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69033 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69042 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69026 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69069 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69044 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69023 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69009 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68960 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=15949.766 E(kin)=631.479 temperature=312.924 | | Etotal =15318.288 grad(E)=63.382 E(BOND)=3539.145 E(ANGL)=1326.294 | | E(DIHE)=0.000 E(IMPR)=1394.804 E(VDW )=3299.330 E(ELEC)=-139.658 | | E(CDIH)=217.680 E(NOE )=5268.746 E(PLAN)=411.947 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69001 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68978 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69002 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69009 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68984 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69003 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69071 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69094 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69103 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69094 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69123 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=15941.003 E(kin)=636.259 temperature=315.293 | | Etotal =15304.745 grad(E)=63.364 E(BOND)=3494.072 E(ANGL)=1288.460 | | E(DIHE)=0.000 E(IMPR)=1437.505 E(VDW )=3408.079 E(ELEC)=-139.108 | | E(CDIH)=186.558 E(NOE )=5216.332 E(PLAN)=412.847 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69061 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69010 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69013 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68994 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68975 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68914 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68916 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69009 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69091 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=15923.199 E(kin)=619.071 temperature=306.776 | | Etotal =15304.129 grad(E)=64.205 E(BOND)=3526.736 E(ANGL)=1321.788 | | E(DIHE)=0.000 E(IMPR)=1417.862 E(VDW )=3371.995 E(ELEC)=-146.338 | | E(CDIH)=191.020 E(NOE )=5203.108 E(PLAN)=417.958 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69166 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69258 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69251 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69313 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69375 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69443 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.39 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69454 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69401 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69353 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69343 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=15940.127 E(kin)=588.671 temperature=291.711 | | Etotal =15351.456 grad(E)=65.714 E(BOND)=3589.481 E(ANGL)=1324.616 | | E(DIHE)=0.000 E(IMPR)=1436.530 E(VDW )=3298.623 E(ELEC)=-136.766 | | E(CDIH)=171.295 E(NOE )=5258.809 E(PLAN)=408.867 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69354 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69372 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69386 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.38 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.47 A apart NBONDS: found 69348 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69317 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69231 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69191 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69108 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69051 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69031 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=15923.518 E(kin)=604.903 temperature=299.755 | | Etotal =15318.615 grad(E)=67.488 E(BOND)=3563.575 E(ANGL)=1300.512 | | E(DIHE)=0.000 E(IMPR)=1444.738 E(VDW )=3379.421 E(ELEC)=-143.416 | | E(CDIH)=187.343 E(NOE )=5177.997 E(PLAN)=408.444 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69081 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69043 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69056 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69096 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69176 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69271 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69270 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69305 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69334 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69344 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=15931.613 E(kin)=615.654 temperature=305.082 | | Etotal =15315.960 grad(E)=64.683 E(BOND)=3578.912 E(ANGL)=1274.627 | | E(DIHE)=0.000 E(IMPR)=1436.302 E(VDW )=3380.093 E(ELEC)=-154.544 | | E(CDIH)=199.448 E(NOE )=5191.152 E(PLAN)=409.968 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69336 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69336 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69276 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69249 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69248 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69227 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69197 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69191 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=15941.656 E(kin)=618.587 temperature=306.536 | | Etotal =15323.069 grad(E)=63.619 E(BOND)=3548.389 E(ANGL)=1276.398 | | E(DIHE)=0.000 E(IMPR)=1459.695 E(VDW )=3347.919 E(ELEC)=-145.530 | | E(CDIH)=225.290 E(NOE )=5203.824 E(PLAN)=407.085 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69150 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69080 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69069 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69093 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69029 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68988 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68996 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=15961.700 E(kin)=583.263 temperature=289.031 | | Etotal =15378.438 grad(E)=68.186 E(BOND)=3559.272 E(ANGL)=1311.986 | | E(DIHE)=0.000 E(IMPR)=1440.432 E(VDW )=3400.098 E(ELEC)=-146.076 | | E(CDIH)=191.196 E(NOE )=5207.313 E(PLAN)=414.216 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68931 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68978 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68903 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68817 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68826 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.40 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68792 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68707 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68679 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=15947.828 E(kin)=602.988 temperature=298.806 | | Etotal =15344.840 grad(E)=69.649 E(BOND)=3630.106 E(ANGL)=1322.546 | | E(DIHE)=0.000 E(IMPR)=1440.083 E(VDW )=3341.876 E(ELEC)=-144.215 | | E(CDIH)=195.842 E(NOE )=5148.418 E(PLAN)=410.185 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68662 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68628 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68677 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68737 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68821 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68890 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68943 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68997 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69087 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=15951.261 E(kin)=619.192 temperature=306.836 | | Etotal =15332.069 grad(E)=65.453 E(BOND)=3553.664 E(ANGL)=1341.939 | | E(DIHE)=0.000 E(IMPR)=1413.201 E(VDW )=3354.863 E(ELEC)=-150.816 | | E(CDIH)=213.931 E(NOE )=5190.928 E(PLAN)=414.358 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15942.998 E(kin)=605.372 temperature=299.987 | | Etotal =15337.626 grad(E)=65.761 E(BOND)=3574.221 E(ANGL)=1327.808 | | E(DIHE)=0.000 E(IMPR)=1423.422 E(VDW )=3339.712 E(ELEC)=-144.515 | | E(CDIH)=196.758 E(NOE )=5210.521 E(PLAN)=409.699 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.757 E(kin)=11.975 temperature=5.934 | | Etotal =17.076 grad(E)=1.345 E(BOND)=35.414 E(ANGL)=25.268 | | E(DIHE)=0.000 E(IMPR)=24.730 E(VDW )=40.361 E(ELEC)=5.180 | | E(CDIH)=12.228 E(NOE )=39.375 E(PLAN)=4.783 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=15941.062 E(kin)=605.285 temperature=299.944 | | Etotal =15335.777 grad(E)=63.168 E(BOND)=3562.652 E(ANGL)=1324.163 | | E(DIHE)=0.000 E(IMPR)=1419.860 E(VDW )=3340.625 E(ELEC)=-138.181 | | E(CDIH)=197.849 E(NOE )=5219.165 E(PLAN)=409.644 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=27.317 E(kin)=13.401 temperature=6.641 | | Etotal =29.096 grad(E)=2.908 E(BOND)=37.742 E(ANGL)=27.450 | | E(DIHE)=0.000 E(IMPR)=27.208 E(VDW )=47.794 E(ELEC)=7.483 | | E(CDIH)=16.151 E(NOE )=43.636 E(PLAN)=6.407 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69153 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69169 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69156 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69120 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69149 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69176 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69226 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69201 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69213 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=15961.392 E(kin)=601.940 temperature=298.287 | | Etotal =15359.452 grad(E)=64.837 E(BOND)=3532.096 E(ANGL)=1350.629 | | E(DIHE)=0.000 E(IMPR)=1420.213 E(VDW )=3357.971 E(ELEC)=-140.602 | | E(CDIH)=204.007 E(NOE )=5217.134 E(PLAN)=418.004 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.38 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69197 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69164 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69143 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69166 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69187 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69163 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69230 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=15958.214 E(kin)=598.502 temperature=296.583 | | Etotal =15359.713 grad(E)=63.685 E(BOND)=3518.090 E(ANGL)=1334.134 | | E(DIHE)=0.000 E(IMPR)=1461.811 E(VDW )=3408.129 E(ELEC)=-138.996 | | E(CDIH)=191.761 E(NOE )=5166.725 E(PLAN)=418.057 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69196 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69230 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69285 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69285 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69277 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69337 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69266 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69203 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=15947.503 E(kin)=588.929 temperature=291.839 | | Etotal =15358.574 grad(E)=66.400 E(BOND)=3584.921 E(ANGL)=1343.325 | | E(DIHE)=0.000 E(IMPR)=1434.508 E(VDW )=3350.283 E(ELEC)=-134.221 | | E(CDIH)=217.020 E(NOE )=5147.806 E(PLAN)=414.932 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69044 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.25 A apart NBONDS: found 68908 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68858 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68837 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=15936.128 E(kin)=616.936 temperature=305.718 | | Etotal =15319.192 grad(E)=64.514 E(BOND)=3662.322 E(ANGL)=1328.597 | | E(DIHE)=0.000 E(IMPR)=1481.255 E(VDW )=3264.096 E(ELEC)=-137.609 | | E(CDIH)=186.271 E(NOE )=5125.007 E(PLAN)=409.255 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68711 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68662 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68642 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.20 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68639 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68660 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68690 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68696 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68708 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68705 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=15955.840 E(kin)=584.459 temperature=289.624 | | Etotal =15371.382 grad(E)=69.768 E(BOND)=3615.116 E(ANGL)=1335.492 | | E(DIHE)=0.000 E(IMPR)=1455.800 E(VDW )=3251.868 E(ELEC)=-144.858 | | E(CDIH)=193.238 E(NOE )=5257.930 E(PLAN)=406.795 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68719 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68741 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68771 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68791 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68789 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 68831 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68861 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68913 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68971 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=15939.998 E(kin)=615.462 temperature=304.987 | | Etotal =15324.536 grad(E)=68.178 E(BOND)=3618.078 E(ANGL)=1328.030 | | E(DIHE)=0.000 E(IMPR)=1450.943 E(VDW )=3358.897 E(ELEC)=-145.941 | | E(CDIH)=198.546 E(NOE )=5106.105 E(PLAN)=409.878 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68996 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69073 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69218 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69442 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69597 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69731 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=15954.689 E(kin)=613.999 temperature=304.262 | | Etotal =15340.690 grad(E)=66.114 E(BOND)=3588.260 E(ANGL)=1294.118 | | E(DIHE)=0.000 E(IMPR)=1470.799 E(VDW )=3326.465 E(ELEC)=-144.169 | | E(CDIH)=201.759 E(NOE )=5187.231 E(PLAN)=416.226 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69780 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69850 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69858 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69780 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69768 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69747 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69746 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69752 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=15941.277 E(kin)=588.918 temperature=291.834 | | Etotal =15352.359 grad(E)=65.974 E(BOND)=3623.135 E(ANGL)=1348.487 | | E(DIHE)=0.000 E(IMPR)=1415.422 E(VDW )=3283.926 E(ELEC)=-134.814 | | E(CDIH)=189.007 E(NOE )=5223.112 E(PLAN)=404.084 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69778 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69878 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69970 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69980 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69990 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70040 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69992 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69994 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69942 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=15940.216 E(kin)=597.272 temperature=295.973 | | Etotal =15342.945 grad(E)=66.318 E(BOND)=3638.200 E(ANGL)=1312.642 | | E(DIHE)=0.000 E(IMPR)=1426.857 E(VDW )=3280.076 E(ELEC)=-139.565 | | E(CDIH)=190.051 E(NOE )=5230.116 E(PLAN)=404.568 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69839 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69738 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.24 A apart NBONDS: found 69699 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69615 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69563 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69529 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69488 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69444 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=15970.845 E(kin)=609.400 temperature=301.983 | | Etotal =15361.445 grad(E)=66.457 E(BOND)=3573.510 E(ANGL)=1333.165 | | E(DIHE)=0.000 E(IMPR)=1401.877 E(VDW )=3307.201 E(ELEC)=-127.994 | | E(CDIH)=190.872 E(NOE )=5276.188 E(PLAN)=406.627 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15947.099 E(kin)=605.392 temperature=299.997 | | Etotal =15341.707 grad(E)=66.221 E(BOND)=3579.450 E(ANGL)=1329.439 | | E(DIHE)=0.000 E(IMPR)=1423.664 E(VDW )=3336.879 E(ELEC)=-139.590 | | E(CDIH)=197.370 E(NOE )=5204.684 E(PLAN)=409.812 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.606 E(kin)=12.340 temperature=6.115 | | Etotal =16.550 grad(E)=1.341 E(BOND)=35.900 E(ANGL)=25.084 | | E(DIHE)=0.000 E(IMPR)=25.210 E(VDW )=40.601 E(ELEC)=4.087 | | E(CDIH)=11.649 E(NOE )=39.116 E(PLAN)=4.574 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=15941.816 E(kin)=605.298 temperature=299.951 | | Etotal =15336.518 grad(E)=63.550 E(BOND)=3564.752 E(ANGL)=1324.822 | | E(DIHE)=0.000 E(IMPR)=1420.336 E(VDW )=3340.156 E(ELEC)=-138.357 | | E(CDIH)=197.789 E(NOE )=5217.355 E(PLAN)=409.665 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=25.957 E(kin)=13.273 temperature=6.578 | | Etotal =27.907 grad(E)=2.940 E(BOND)=37.926 E(ANGL)=27.222 | | E(DIHE)=0.000 E(IMPR)=26.996 E(VDW )=46.971 E(ELEC)=7.163 | | E(CDIH)=15.660 E(NOE )=43.362 E(PLAN)=6.208 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.46 A apart NBONDS: found 69389 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69338 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69409 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69479 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69563 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69697 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=15947.842 E(kin)=604.086 temperature=299.350 | | Etotal =15343.755 grad(E)=68.245 E(BOND)=3574.633 E(ANGL)=1316.285 | | E(DIHE)=0.000 E(IMPR)=1404.930 E(VDW )=3387.775 E(ELEC)=-139.582 | | E(CDIH)=207.029 E(NOE )=5184.062 E(PLAN)=408.622 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69855 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69909 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69908 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.25 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69847 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.41 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69812 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69716 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.18 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69687 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=15934.055 E(kin)=606.822 temperature=300.706 | | Etotal =15327.234 grad(E)=65.185 E(BOND)=3560.254 E(ANGL)=1317.924 | | E(DIHE)=0.000 E(IMPR)=1414.139 E(VDW )=3395.283 E(ELEC)=-135.381 | | E(CDIH)=179.776 E(NOE )=5181.647 E(PLAN)=413.591 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69644 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69661 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69628 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69603 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69557 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69506 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69425 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=15940.688 E(kin)=586.476 temperature=290.623 | | Etotal =15354.212 grad(E)=66.063 E(BOND)=3542.833 E(ANGL)=1313.757 | | E(DIHE)=0.000 E(IMPR)=1448.488 E(VDW )=3348.388 E(ELEC)=-142.450 | | E(CDIH)=205.309 E(NOE )=5227.749 E(PLAN)=410.139 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69409 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.27 A apart NBONDS: found 69397 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69364 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69374 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69382 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69397 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69400 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=15948.422 E(kin)=600.195 temperature=297.422 | | Etotal =15348.227 grad(E)=66.645 E(BOND)=3597.193 E(ANGL)=1335.393 | | E(DIHE)=0.000 E(IMPR)=1427.542 E(VDW )=3313.684 E(ELEC)=-147.343 | | E(CDIH)=191.604 E(NOE )=5217.014 E(PLAN)=413.140 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69399 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69370 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69388 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69356 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69339 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69410 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=15942.707 E(kin)=605.680 temperature=300.140 | | Etotal =15337.026 grad(E)=66.476 E(BOND)=3519.410 E(ANGL)=1317.938 | | E(DIHE)=0.000 E(IMPR)=1404.084 E(VDW )=3407.695 E(ELEC)=-136.479 | | E(CDIH)=198.572 E(NOE )=5210.482 E(PLAN)=415.324 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69481 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69492 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69480 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69493 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69396 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69205 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=15945.836 E(kin)=596.208 temperature=295.446 | | Etotal =15349.628 grad(E)=67.311 E(BOND)=3555.603 E(ANGL)=1354.351 | | E(DIHE)=0.000 E(IMPR)=1423.454 E(VDW )=3341.893 E(ELEC)=-147.973 | | E(CDIH)=210.237 E(NOE )=5210.779 E(PLAN)=401.286 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69179 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69143 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69003 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69000 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69032 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=15967.169 E(kin)=625.578 temperature=310.000 | | Etotal =15341.591 grad(E)=65.274 E(BOND)=3612.752 E(ANGL)=1364.512 | | E(DIHE)=0.000 E(IMPR)=1414.282 E(VDW )=3320.299 E(ELEC)=-142.092 | | E(CDIH)=199.895 E(NOE )=5166.520 E(PLAN)=405.423 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69142 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69118 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69119 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69192 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69247 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69283 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69334 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=15944.166 E(kin)=596.127 temperature=295.406 | | Etotal =15348.039 grad(E)=67.316 E(BOND)=3563.087 E(ANGL)=1385.868 | | E(DIHE)=0.000 E(IMPR)=1349.345 E(VDW )=3346.123 E(ELEC)=-152.778 | | E(CDIH)=195.352 E(NOE )=5254.854 E(PLAN)=406.188 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69349 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69314 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69307 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69315 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69306 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69359 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=15956.907 E(kin)=598.240 temperature=296.453 | | Etotal =15358.667 grad(E)=68.161 E(BOND)=3566.878 E(ANGL)=1376.144 | | E(DIHE)=0.000 E(IMPR)=1417.886 E(VDW )=3309.247 E(ELEC)=-142.287 | | E(CDIH)=184.500 E(NOE )=5237.922 E(PLAN)=408.377 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69406 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69471 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69460 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69479 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69471 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69441 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69361 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=15951.682 E(kin)=611.078 temperature=302.815 | | Etotal =15340.604 grad(E)=67.758 E(BOND)=3577.313 E(ANGL)=1329.383 | | E(DIHE)=0.000 E(IMPR)=1451.754 E(VDW )=3317.170 E(ELEC)=-147.512 | | E(CDIH)=204.971 E(NOE )=5199.527 E(PLAN)=407.997 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15948.316 E(kin)=605.544 temperature=300.072 | | Etotal =15342.772 grad(E)=66.559 E(BOND)=3581.305 E(ANGL)=1333.264 | | E(DIHE)=0.000 E(IMPR)=1422.207 E(VDW )=3335.676 E(ELEC)=-142.244 | | E(CDIH)=196.934 E(NOE )=5206.289 E(PLAN)=409.341 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.251 E(kin)=12.771 temperature=6.328 | | Etotal =16.496 grad(E)=1.395 E(BOND)=37.796 E(ANGL)=25.047 | | E(DIHE)=0.000 E(IMPR)=24.359 E(VDW )=39.401 E(ELEC)=5.507 | | E(CDIH)=12.372 E(NOE )=35.767 E(PLAN)=4.469 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=15942.539 E(kin)=605.325 temperature=299.964 | | Etotal =15337.213 grad(E)=63.884 E(BOND)=3566.591 E(ANGL)=1325.760 | | E(DIHE)=0.000 E(IMPR)=1420.543 E(VDW )=3339.659 E(ELEC)=-138.789 | | E(CDIH)=197.694 E(NOE )=5216.125 E(PLAN)=409.629 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=24.842 E(kin)=13.219 temperature=6.550 | | Etotal =26.952 grad(E)=2.965 E(BOND)=38.266 E(ANGL)=27.119 | | E(DIHE)=0.000 E(IMPR)=26.722 E(VDW )=46.213 E(ELEC)=7.104 | | E(CDIH)=15.332 E(NOE )=42.727 E(PLAN)=6.040 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69205 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69109 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68942 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68887 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68834 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68828 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68832 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68814 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=15942.841 E(kin)=586.891 temperature=290.829 | | Etotal =15355.949 grad(E)=66.778 E(BOND)=3639.184 E(ANGL)=1326.438 | | E(DIHE)=0.000 E(IMPR)=1357.134 E(VDW )=3295.698 E(ELEC)=-142.541 | | E(CDIH)=208.850 E(NOE )=5259.857 E(PLAN)=411.330 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68793 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68857 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68868 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68904 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 68916 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68896 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68874 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68862 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=15956.143 E(kin)=618.493 temperature=306.489 | | Etotal =15337.651 grad(E)=67.505 E(BOND)=3577.030 E(ANGL)=1332.540 | | E(DIHE)=0.000 E(IMPR)=1356.774 E(VDW )=3328.718 E(ELEC)=-137.049 | | E(CDIH)=211.716 E(NOE )=5252.568 E(PLAN)=415.354 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68873 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68970 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69003 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69020 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69127 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69239 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69433 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=15949.476 E(kin)=621.112 temperature=307.787 | | Etotal =15328.363 grad(E)=65.346 E(BOND)=3580.014 E(ANGL)=1318.841 | | E(DIHE)=0.000 E(IMPR)=1396.952 E(VDW )=3311.483 E(ELEC)=-142.215 | | E(CDIH)=202.500 E(NOE )=5250.209 E(PLAN)=410.580 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69461 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.18 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69418 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69405 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69392 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69398 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69368 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69354 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=15947.671 E(kin)=594.767 temperature=294.732 | | Etotal =15352.903 grad(E)=68.743 E(BOND)=3637.090 E(ANGL)=1323.404 | | E(DIHE)=0.000 E(IMPR)=1473.593 E(VDW )=3248.333 E(ELEC)=-143.493 | | E(CDIH)=191.578 E(NOE )=5207.999 E(PLAN)=414.399 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69421 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69419 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69370 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69400 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69474 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=15935.693 E(kin)=598.361 temperature=296.513 | | Etotal =15337.332 grad(E)=67.722 E(BOND)=3563.854 E(ANGL)=1339.988 | | E(DIHE)=0.000 E(IMPR)=1409.051 E(VDW )=3349.315 E(ELEC)=-150.286 | | E(CDIH)=210.386 E(NOE )=5207.633 E(PLAN)=407.390 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69501 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69564 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69523 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69520 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69572 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69565 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=15927.469 E(kin)=604.932 temperature=299.769 | | Etotal =15322.537 grad(E)=63.959 E(BOND)=3588.870 E(ANGL)=1328.073 | | E(DIHE)=0.000 E(IMPR)=1439.830 E(VDW )=3288.391 E(ELEC)=-153.105 | | E(CDIH)=199.352 E(NOE )=5218.055 E(PLAN)=413.070 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69530 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69443 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69389 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69373 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69404 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69412 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69338 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=15941.621 E(kin)=592.366 temperature=293.542 | | Etotal =15349.254 grad(E)=68.824 E(BOND)=3627.475 E(ANGL)=1331.426 | | E(DIHE)=0.000 E(IMPR)=1414.851 E(VDW )=3322.580 E(ELEC)=-143.892 | | E(CDIH)=201.006 E(NOE )=5187.648 E(PLAN)=408.161 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69257 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69260 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69180 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69150 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69139 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69181 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69113 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=15951.967 E(kin)=613.601 temperature=304.065 | | Etotal =15338.366 grad(E)=66.115 E(BOND)=3604.469 E(ANGL)=1321.541 | | E(DIHE)=0.000 E(IMPR)=1407.474 E(VDW )=3329.006 E(ELEC)=-140.317 | | E(CDIH)=213.754 E(NOE )=5196.528 E(PLAN)=405.911 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69110 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69132 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69236 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69272 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69303 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.49 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69254 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=15952.383 E(kin)=596.121 temperature=295.403 | | Etotal =15356.261 grad(E)=69.402 E(BOND)=3564.321 E(ANGL)=1330.068 | | E(DIHE)=0.000 E(IMPR)=1446.439 E(VDW )=3352.897 E(ELEC)=-141.026 | | E(CDIH)=166.774 E(NOE )=5225.157 E(PLAN)=411.630 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69194 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69097 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69088 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69083 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69065 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69046 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68987 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68955 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=15933.122 E(kin)=605.133 temperature=299.869 | | Etotal =15327.990 grad(E)=67.922 E(BOND)=3548.971 E(ANGL)=1323.454 | | E(DIHE)=0.000 E(IMPR)=1458.588 E(VDW )=3297.332 E(ELEC)=-138.975 | | E(CDIH)=204.987 E(NOE )=5221.696 E(PLAN)=411.936 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15942.048 E(kin)=605.548 temperature=300.074 | | Etotal =15336.500 grad(E)=67.320 E(BOND)=3580.980 E(ANGL)=1332.053 | | E(DIHE)=0.000 E(IMPR)=1423.429 E(VDW )=3338.956 E(ELEC)=-143.642 | | E(CDIH)=197.268 E(NOE )=5197.395 E(PLAN)=410.062 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.123 E(kin)=12.774 temperature=6.330 | | Etotal =15.777 grad(E)=1.338 E(BOND)=37.027 E(ANGL)=23.517 | | E(DIHE)=0.000 E(IMPR)=26.421 E(VDW )=40.771 E(ELEC)=4.659 | | E(CDIH)=13.903 E(NOE )=36.309 E(PLAN)=4.540 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=15942.490 E(kin)=605.348 temperature=299.975 | | Etotal =15337.142 grad(E)=64.228 E(BOND)=3568.030 E(ANGL)=1326.390 | | E(DIHE)=0.000 E(IMPR)=1420.832 E(VDW )=3339.588 E(ELEC)=-139.274 | | E(CDIH)=197.651 E(NOE )=5214.252 E(PLAN)=409.672 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=23.784 E(kin)=13.175 temperature=6.529 | | Etotal =26.052 grad(E)=3.026 E(BOND)=38.388 E(ANGL)=26.847 | | E(DIHE)=0.000 E(IMPR)=26.706 E(VDW )=45.698 E(ELEC)=7.051 | | E(CDIH)=15.195 E(NOE )=42.502 E(PLAN)=5.909 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68959 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69067 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69038 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69030 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68946 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 68831 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=15935.456 E(kin)=606.232 temperature=300.413 | | Etotal =15329.224 grad(E)=69.185 E(BOND)=3542.563 E(ANGL)=1328.967 | | E(DIHE)=0.000 E(IMPR)=1455.596 E(VDW )=3359.768 E(ELEC)=-147.497 | | E(CDIH)=183.421 E(NOE )=5200.856 E(PLAN)=405.551 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68767 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68690 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68697 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68776 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68903 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68930 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=15943.441 E(kin)=604.373 temperature=299.492 | | Etotal =15339.069 grad(E)=69.965 E(BOND)=3520.771 E(ANGL)=1313.305 | | E(DIHE)=0.000 E(IMPR)=1413.477 E(VDW )=3424.062 E(ELEC)=-149.048 | | E(CDIH)=192.674 E(NOE )=5221.529 E(PLAN)=402.297 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69021 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69153 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69192 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69249 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69308 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69347 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=15943.621 E(kin)=602.839 temperature=298.732 | | Etotal =15340.782 grad(E)=69.418 E(BOND)=3616.221 E(ANGL)=1339.057 | | E(DIHE)=0.000 E(IMPR)=1432.050 E(VDW )=3366.091 E(ELEC)=-147.304 | | E(CDIH)=172.459 E(NOE )=5150.620 E(PLAN)=411.587 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69316 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69282 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69217 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69142 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.24 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69082 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69001 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68897 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=15933.474 E(kin)=601.903 temperature=298.268 | | Etotal =15331.571 grad(E)=68.014 E(BOND)=3561.330 E(ANGL)=1318.213 | | E(DIHE)=0.000 E(IMPR)=1400.092 E(VDW )=3354.796 E(ELEC)=-138.793 | | E(CDIH)=178.377 E(NOE )=5247.790 E(PLAN)=409.766 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68878 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68819 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68910 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68864 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68826 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68763 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68699 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=15944.949 E(kin)=609.656 temperature=302.110 | | Etotal =15335.293 grad(E)=66.987 E(BOND)=3533.483 E(ANGL)=1310.818 | | E(DIHE)=0.000 E(IMPR)=1462.364 E(VDW )=3336.346 E(ELEC)=-136.236 | | E(CDIH)=176.674 E(NOE )=5236.687 E(PLAN)=415.157 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68573 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68586 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68547 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68575 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68572 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68649 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68631 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=15956.023 E(kin)=597.399 temperature=296.036 | | Etotal =15358.624 grad(E)=69.275 E(BOND)=3597.528 E(ANGL)=1367.165 | | E(DIHE)=0.000 E(IMPR)=1434.983 E(VDW )=3317.067 E(ELEC)=-140.765 | | E(CDIH)=171.182 E(NOE )=5205.944 E(PLAN)=405.520 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68554 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68496 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68444 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68469 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68365 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=15930.511 E(kin)=614.103 temperature=304.314 | | Etotal =15316.407 grad(E)=65.305 E(BOND)=3538.314 E(ANGL)=1342.366 | | E(DIHE)=0.000 E(IMPR)=1440.344 E(VDW )=3335.921 E(ELEC)=-146.435 | | E(CDIH)=193.597 E(NOE )=5199.876 E(PLAN)=412.423 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68247 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68221 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68144 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.39 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68100 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 67939 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 67928 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=15937.846 E(kin)=620.294 temperature=307.382 | | Etotal =15317.552 grad(E)=68.032 E(BOND)=3544.642 E(ANGL)=1311.705 | | E(DIHE)=0.000 E(IMPR)=1423.997 E(VDW )=3395.839 E(ELEC)=-145.979 | | E(CDIH)=198.748 E(NOE )=5184.793 E(PLAN)=403.808 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 67913 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 67976 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 67968 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68075 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68096 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68174 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68240 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68345 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=15940.878 E(kin)=597.120 temperature=295.898 | | Etotal =15343.757 grad(E)=68.848 E(BOND)=3641.101 E(ANGL)=1322.905 | | E(DIHE)=0.000 E(IMPR)=1451.279 E(VDW )=3304.720 E(ELEC)=-152.109 | | E(CDIH)=189.736 E(NOE )=5184.980 E(PLAN)=401.146 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68357 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68416 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68426 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68480 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68546 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 68610 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68633 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68719 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=15936.922 E(kin)=603.699 temperature=299.158 | | Etotal =15333.223 grad(E)=67.673 E(BOND)=3555.610 E(ANGL)=1339.947 | | E(DIHE)=0.000 E(IMPR)=1441.910 E(VDW )=3282.879 E(ELEC)=-146.679 | | E(CDIH)=184.931 E(NOE )=5263.682 E(PLAN)=410.943 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15941.083 E(kin)=605.462 temperature=300.032 | | Etotal =15335.621 grad(E)=68.148 E(BOND)=3580.124 E(ANGL)=1332.441 | | E(DIHE)=0.000 E(IMPR)=1426.439 E(VDW )=3335.735 E(ELEC)=-145.493 | | E(CDIH)=195.966 E(NOE )=5201.063 E(PLAN)=409.346 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.213 E(kin)=12.590 temperature=6.239 | | Etotal =15.107 grad(E)=1.461 E(BOND)=38.455 E(ANGL)=23.554 | | E(DIHE)=0.000 E(IMPR)=25.949 E(VDW )=41.785 E(ELEC)=4.968 | | E(CDIH)=11.970 E(NOE )=37.283 E(PLAN)=4.309 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=15942.362 E(kin)=605.358 temperature=299.980 | | Etotal =15337.004 grad(E)=64.584 E(BOND)=3569.130 E(ANGL)=1326.940 | | E(DIHE)=0.000 E(IMPR)=1421.342 E(VDW )=3339.238 E(ELEC)=-139.839 | | E(CDIH)=197.498 E(NOE )=5213.053 E(PLAN)=409.642 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=22.851 E(kin)=13.123 temperature=6.503 | | Etotal =25.257 grad(E)=3.128 E(BOND)=38.551 E(ANGL)=26.621 | | E(DIHE)=0.000 E(IMPR)=26.687 E(VDW )=45.370 E(ELEC)=7.116 | | E(CDIH)=14.939 E(NOE )=42.225 E(PLAN)=5.783 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68775 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68941 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69081 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69067 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69058 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69056 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69058 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69134 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69136 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69134 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=15965.320 E(kin)=594.893 temperature=294.795 | | Etotal =15370.427 grad(E)=69.401 E(BOND)=3531.560 E(ANGL)=1385.184 | | E(DIHE)=0.000 E(IMPR)=1374.953 E(VDW )=3403.596 E(ELEC)=-142.645 | | E(CDIH)=185.182 E(NOE )=5221.781 E(PLAN)=410.817 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69144 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.37 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69128 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69139 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.46 A apart NBONDS: found 69043 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68947 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68904 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68864 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68839 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.49 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.39 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68819 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=15932.901 E(kin)=591.381 temperature=293.054 | | Etotal =15341.521 grad(E)=67.720 E(BOND)=3608.198 E(ANGL)=1339.048 | | E(DIHE)=0.000 E(IMPR)=1350.625 E(VDW )=3309.775 E(ELEC)=-149.836 | | E(CDIH)=200.716 E(NOE )=5270.951 E(PLAN)=412.045 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68859 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68820 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68766 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68751 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.18 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68692 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68580 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68510 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=15927.884 E(kin)=605.322 temperature=299.963 | | Etotal =15322.562 grad(E)=68.167 E(BOND)=3646.373 E(ANGL)=1326.724 | | E(DIHE)=0.000 E(IMPR)=1408.649 E(VDW )=3282.612 E(ELEC)=-144.913 | | E(CDIH)=197.930 E(NOE )=5193.034 E(PLAN)=412.152 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68394 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68334 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68244 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68197 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68180 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68222 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68238 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=15932.240 E(kin)=564.305 temperature=279.637 | | Etotal =15367.934 grad(E)=69.677 E(BOND)=3600.432 E(ANGL)=1333.159 | | E(DIHE)=0.000 E(IMPR)=1436.606 E(VDW )=3377.533 E(ELEC)=-150.451 | | E(CDIH)=203.187 E(NOE )=5156.971 E(PLAN)=410.498 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.40 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68183 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68189 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68214 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.40 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68221 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68284 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68279 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68243 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68278 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=15938.393 E(kin)=608.025 temperature=301.302 | | Etotal =15330.368 grad(E)=68.807 E(BOND)=3587.879 E(ANGL)=1352.958 | | E(DIHE)=0.000 E(IMPR)=1431.454 E(VDW )=3310.027 E(ELEC)=-146.965 | | E(CDIH)=191.071 E(NOE )=5191.082 E(PLAN)=412.862 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68298 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68349 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68375 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 68442 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68512 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68522 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68517 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68540 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68569 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=15955.190 E(kin)=607.687 temperature=301.134 | | Etotal =15347.503 grad(E)=68.116 E(BOND)=3613.386 E(ANGL)=1330.068 | | E(DIHE)=0.000 E(IMPR)=1445.532 E(VDW )=3320.714 E(ELEC)=-146.112 | | E(CDIH)=211.216 E(NOE )=5157.541 E(PLAN)=415.158 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68535 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68512 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68499 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68488 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68525 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68584 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68666 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=15950.146 E(kin)=610.979 temperature=302.766 | | Etotal =15339.167 grad(E)=68.060 E(BOND)=3569.690 E(ANGL)=1328.284 | | E(DIHE)=0.000 E(IMPR)=1458.903 E(VDW )=3331.833 E(ELEC)=-143.609 | | E(CDIH)=185.144 E(NOE )=5201.800 E(PLAN)=407.122 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68693 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68634 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68575 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68598 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68605 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68501 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68451 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=15924.338 E(kin)=600.567 temperature=297.606 | | Etotal =15323.770 grad(E)=68.364 E(BOND)=3652.991 E(ANGL)=1374.177 | | E(DIHE)=0.000 E(IMPR)=1422.935 E(VDW )=3276.929 E(ELEC)=-155.069 | | E(CDIH)=187.654 E(NOE )=5151.371 E(PLAN)=412.783 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68412 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68294 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68244 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68217 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68083 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68010 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68008 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 67969 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=15935.834 E(kin)=612.303 temperature=303.422 | | Etotal =15323.531 grad(E)=66.850 E(BOND)=3594.819 E(ANGL)=1344.739 | | E(DIHE)=0.000 E(IMPR)=1422.201 E(VDW )=3313.337 E(ELEC)=-148.386 | | E(CDIH)=196.219 E(NOE )=5186.572 E(PLAN)=414.030 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 67954 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 67965 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68047 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68044 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68058 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 68132 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.47 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68196 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68189 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=15934.025 E(kin)=611.134 temperature=302.842 | | Etotal =15322.891 grad(E)=67.654 E(BOND)=3544.663 E(ANGL)=1296.411 | | E(DIHE)=0.000 E(IMPR)=1423.329 E(VDW )=3349.860 E(ELEC)=-145.698 | | E(CDIH)=176.471 E(NOE )=5271.544 E(PLAN)=406.311 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15943.365 E(kin)=605.498 temperature=300.049 | | Etotal =15337.867 grad(E)=68.233 E(BOND)=3579.978 E(ANGL)=1334.302 | | E(DIHE)=0.000 E(IMPR)=1420.695 E(VDW )=3343.965 E(ELEC)=-146.302 | | E(CDIH)=197.457 E(NOE )=5197.165 E(PLAN)=410.609 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.753 E(kin)=13.007 temperature=6.445 | | Etotal =17.817 grad(E)=1.470 E(BOND)=40.743 E(ANGL)=23.558 | | E(DIHE)=0.000 E(IMPR)=26.889 E(VDW )=43.623 E(ELEC)=3.224 | | E(CDIH)=12.700 E(NOE )=36.755 E(PLAN)=4.305 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=15942.445 E(kin)=605.370 temperature=299.986 | | Etotal =15337.076 grad(E)=64.888 E(BOND)=3570.034 E(ANGL)=1327.553 | | E(DIHE)=0.000 E(IMPR)=1421.288 E(VDW )=3339.632 E(ELEC)=-140.378 | | E(CDIH)=197.495 E(NOE )=5211.729 E(PLAN)=409.723 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=22.187 E(kin)=13.113 temperature=6.498 | | Etotal =24.724 grad(E)=3.189 E(BOND)=38.854 E(ANGL)=26.458 | | E(DIHE)=0.000 E(IMPR)=26.704 E(VDW )=45.246 E(ELEC)=7.104 | | E(CDIH)=14.765 E(NOE )=42.027 E(PLAN)=5.680 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68287 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68342 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68399 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68379 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 68376 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68381 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68401 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H8 " only 1.44 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68422 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H8 " only 1.42 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68433 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=15938.920 E(kin)=603.706 temperature=299.162 | | Etotal =15335.214 grad(E)=69.416 E(BOND)=3596.739 E(ANGL)=1330.058 | | E(DIHE)=0.000 E(IMPR)=1382.536 E(VDW )=3290.443 E(ELEC)=-156.346 | | E(CDIH)=215.859 E(NOE )=5271.352 E(PLAN)=404.573 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68482 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68532 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68500 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68565 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68528 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68374 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.39 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68161 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=15959.535 E(kin)=630.574 temperature=312.476 | | Etotal =15328.960 grad(E)=66.186 E(BOND)=3588.250 E(ANGL)=1323.193 | | E(DIHE)=0.000 E(IMPR)=1411.635 E(VDW )=3345.834 E(ELEC)=-140.661 | | E(CDIH)=179.497 E(NOE )=5218.582 E(PLAN)=402.630 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68149 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68198 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68113 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68085 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68083 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68091 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68113 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.29 A apart NBONDS: found 68124 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68077 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68046 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=15927.033 E(kin)=616.827 temperature=305.664 | | Etotal =15310.206 grad(E)=66.046 E(BOND)=3563.423 E(ANGL)=1314.596 | | E(DIHE)=0.000 E(IMPR)=1431.687 E(VDW )=3352.373 E(ELEC)=-146.889 | | E(CDIH)=198.687 E(NOE )=5189.446 E(PLAN)=406.882 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68049 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68073 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.22 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68125 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68042 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68039 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68049 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68065 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68073 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=15927.902 E(kin)=612.591 temperature=303.565 | | Etotal =15315.310 grad(E)=67.165 E(BOND)=3606.562 E(ANGL)=1347.381 | | E(DIHE)=0.000 E(IMPR)=1384.632 E(VDW )=3291.235 E(ELEC)=-150.280 | | E(CDIH)=181.588 E(NOE )=5247.789 E(PLAN)=406.402 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68141 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68173 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68183 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68279 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.41 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68347 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 68341 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68352 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=15946.999 E(kin)=614.810 temperature=304.664 | | Etotal =15332.190 grad(E)=69.032 E(BOND)=3548.607 E(ANGL)=1322.139 | | E(DIHE)=0.000 E(IMPR)=1420.449 E(VDW )=3355.820 E(ELEC)=-149.094 | | E(CDIH)=203.511 E(NOE )=5221.073 E(PLAN)=409.684 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68334 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68286 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68292 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68394 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68494 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=15939.080 E(kin)=619.971 temperature=307.222 | | Etotal =15319.109 grad(E)=67.305 E(BOND)=3615.757 E(ANGL)=1364.729 | | E(DIHE)=0.000 E(IMPR)=1420.210 E(VDW )=3341.374 E(ELEC)=-149.081 | | E(CDIH)=183.994 E(NOE )=5140.662 E(PLAN)=401.466 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68599 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68579 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68573 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68537 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68580 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68620 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68635 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=15951.050 E(kin)=596.079 temperature=295.382 | | Etotal =15354.971 grad(E)=69.944 E(BOND)=3597.267 E(ANGL)=1348.780 | | E(DIHE)=0.000 E(IMPR)=1468.193 E(VDW )=3279.871 E(ELEC)=-143.871 | | E(CDIH)=180.047 E(NOE )=5215.647 E(PLAN)=409.037 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68606 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68601 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68610 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.37 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68571 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68600 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=15957.947 E(kin)=618.557 temperature=306.521 | | Etotal =15339.389 grad(E)=68.382 E(BOND)=3589.022 E(ANGL)=1368.782 | | E(DIHE)=0.000 E(IMPR)=1442.593 E(VDW )=3284.407 E(ELEC)=-143.288 | | E(CDIH)=212.146 E(NOE )=5182.863 E(PLAN)=402.865 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68702 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68686 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68766 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68850 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68801 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68816 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 68843 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68763 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=15942.121 E(kin)=603.563 temperature=299.091 | | Etotal =15338.558 grad(E)=68.400 E(BOND)=3637.355 E(ANGL)=1329.092 | | E(DIHE)=0.000 E(IMPR)=1450.938 E(VDW )=3271.497 E(ELEC)=-142.607 | | E(CDIH)=200.231 E(NOE )=5180.472 E(PLAN)=411.581 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68710 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 68767 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68858 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68967 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.27 A apart NBONDS: found 68973 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69060 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.46 A apart NBONDS: found 69036 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=15936.375 E(kin)=606.697 temperature=300.644 | | Etotal =15329.679 grad(E)=68.285 E(BOND)=3599.583 E(ANGL)=1297.131 | | E(DIHE)=0.000 E(IMPR)=1340.008 E(VDW )=3389.960 E(ELEC)=-146.077 | | E(CDIH)=223.733 E(NOE )=5216.944 E(PLAN)=408.398 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15941.955 E(kin)=605.471 temperature=300.036 | | Etotal =15336.484 grad(E)=68.189 E(BOND)=3587.078 E(ANGL)=1328.675 | | E(DIHE)=0.000 E(IMPR)=1426.668 E(VDW )=3334.682 E(ELEC)=-147.143 | | E(CDIH)=195.747 E(NOE )=5201.684 E(PLAN)=409.093 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.992 E(kin)=12.723 temperature=6.305 | | Etotal =15.720 grad(E)=1.458 E(BOND)=35.919 E(ANGL)=24.221 | | E(DIHE)=0.000 E(IMPR)=25.329 E(VDW )=40.310 E(ELEC)=4.353 | | E(CDIH)=13.593 E(NOE )=34.781 E(PLAN)=4.047 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=15942.407 E(kin)=605.377 temperature=299.990 | | Etotal =15337.030 grad(E)=65.142 E(BOND)=3571.345 E(ANGL)=1327.639 | | E(DIHE)=0.000 E(IMPR)=1421.702 E(VDW )=3339.251 E(ELEC)=-140.898 | | E(CDIH)=197.360 E(NOE )=5210.957 E(PLAN)=409.675 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=21.496 E(kin)=13.084 temperature=6.484 | | Etotal =24.151 grad(E)=3.213 E(BOND)=38.902 E(ANGL)=26.294 | | E(DIHE)=0.000 E(IMPR)=26.640 E(VDW )=44.905 E(ELEC)=7.162 | | E(CDIH)=14.686 E(NOE )=41.600 E(PLAN)=5.574 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68984 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69001 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68960 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68968 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69028 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69079 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69146 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69186 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=15938.612 E(kin)=610.050 temperature=302.306 | | Etotal =15328.562 grad(E)=68.996 E(BOND)=3651.935 E(ANGL)=1327.225 | | E(DIHE)=0.000 E(IMPR)=1394.563 E(VDW )=3338.365 E(ELEC)=-147.875 | | E(CDIH)=188.915 E(NOE )=5161.342 E(PLAN)=414.091 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69200 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69159 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69098 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69051 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69007 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68941 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68878 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 68855 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=15921.910 E(kin)=594.595 temperature=294.647 | | Etotal =15327.315 grad(E)=68.493 E(BOND)=3587.599 E(ANGL)=1296.119 | | E(DIHE)=0.000 E(IMPR)=1413.956 E(VDW )=3340.675 E(ELEC)=-145.289 | | E(CDIH)=187.655 E(NOE )=5237.652 E(PLAN)=408.949 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68893 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68922 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69032 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 68981 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.39 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 68944 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68944 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69020 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69105 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=15934.276 E(kin)=592.068 temperature=293.394 | | Etotal =15342.209 grad(E)=69.007 E(BOND)=3607.022 E(ANGL)=1304.445 | | E(DIHE)=0.000 E(IMPR)=1415.044 E(VDW )=3347.043 E(ELEC)=-138.557 | | E(CDIH)=209.324 E(NOE )=5189.074 E(PLAN)=408.814 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69230 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69265 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69284 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69342 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H8 " only 1.50 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69406 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69361 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=15927.493 E(kin)=613.329 temperature=303.930 | | Etotal =15314.164 grad(E)=69.184 E(BOND)=3612.981 E(ANGL)=1292.880 | | E(DIHE)=0.000 E(IMPR)=1443.891 E(VDW )=3356.574 E(ELEC)=-147.220 | | E(CDIH)=194.545 E(NOE )=5149.374 E(PLAN)=411.138 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69229 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69079 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 68997 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68978 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.44 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68952 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68944 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68914 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=15959.879 E(kin)=624.488 temperature=309.460 | | Etotal =15335.390 grad(E)=67.004 E(BOND)=3599.142 E(ANGL)=1299.445 | | E(DIHE)=0.000 E(IMPR)=1461.436 E(VDW )=3273.767 E(ELEC)=-148.572 | | E(CDIH)=229.804 E(NOE )=5213.697 E(PLAN)=406.670 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 68849 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68821 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 68849 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 68893 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 68798 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=15941.157 E(kin)=584.564 temperature=289.676 | | Etotal =15356.593 grad(E)=69.147 E(BOND)=3650.589 E(ANGL)=1371.519 | | E(DIHE)=0.000 E(IMPR)=1428.669 E(VDW )=3297.920 E(ELEC)=-146.916 | | E(CDIH)=193.442 E(NOE )=5160.876 E(PLAN)=400.494 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 68780 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 68828 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 68992 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69111 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69140 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69160 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=15935.672 E(kin)=591.437 temperature=293.082 | | Etotal =15344.235 grad(E)=71.019 E(BOND)=3608.819 E(ANGL)=1336.634 | | E(DIHE)=0.000 E(IMPR)=1419.281 E(VDW )=3268.284 E(ELEC)=-145.896 | | E(CDIH)=209.978 E(NOE )=5236.272 E(PLAN)=410.862 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69122 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69112 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.38 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69243 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69266 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69254 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69304 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=15935.911 E(kin)=608.435 temperature=301.505 | | Etotal =15327.476 grad(E)=69.604 E(BOND)=3518.987 E(ANGL)=1345.939 | | E(DIHE)=0.000 E(IMPR)=1419.638 E(VDW )=3399.228 E(ELEC)=-140.815 | | E(CDIH)=194.617 E(NOE )=5177.538 E(PLAN)=412.344 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.43 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69298 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69311 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69302 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69361 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69383 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69445 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=15937.220 E(kin)=591.654 temperature=293.189 | | Etotal =15345.566 grad(E)=70.480 E(BOND)=3576.963 E(ANGL)=1350.416 | | E(DIHE)=0.000 E(IMPR)=1424.619 E(VDW )=3374.033 E(ELEC)=-148.876 | | E(CDIH)=181.563 E(NOE )=5170.677 E(PLAN)=416.172 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69515 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.38 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69549 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.40 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69492 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69407 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.37 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69425 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=15937.794 E(kin)=598.459 temperature=296.561 | | Etotal =15339.335 grad(E)=70.158 E(BOND)=3639.546 E(ANGL)=1315.127 | | E(DIHE)=0.000 E(IMPR)=1434.282 E(VDW )=3323.204 E(ELEC)=-146.415 | | E(CDIH)=192.511 E(NOE )=5172.742 E(PLAN)=408.338 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15941.397 E(kin)=605.466 temperature=300.034 | | Etotal =15335.930 grad(E)=68.845 E(BOND)=3591.985 E(ANGL)=1324.825 | | E(DIHE)=0.000 E(IMPR)=1427.074 E(VDW )=3333.021 E(ELEC)=-145.476 | | E(CDIH)=196.578 E(NOE )=5198.323 E(PLAN)=409.599 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.078 E(kin)=12.526 temperature=6.207 | | Etotal =15.038 grad(E)=1.533 E(BOND)=35.653 E(ANGL)=23.758 | | E(DIHE)=0.000 E(IMPR)=27.844 E(VDW )=43.556 E(ELEC)=4.373 | | E(CDIH)=12.520 E(NOE )=40.779 E(PLAN)=4.624 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=15942.335 E(kin)=605.384 temperature=299.993 | | Etotal =15336.951 grad(E)=65.406 E(BOND)=3572.819 E(ANGL)=1327.438 | | E(DIHE)=0.000 E(IMPR)=1422.085 E(VDW )=3338.806 E(ELEC)=-141.225 | | E(CDIH)=197.304 E(NOE )=5210.054 E(PLAN)=409.669 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=20.858 E(kin)=13.045 temperature=6.464 | | Etotal =23.619 grad(E)=3.265 E(BOND)=39.043 E(ANGL)=26.131 | | E(DIHE)=0.000 E(IMPR)=26.763 E(VDW )=44.839 E(ELEC)=7.098 | | E(CDIH)=14.543 E(NOE )=41.669 E(PLAN)=5.512 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69372 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69326 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69289 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69370 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=15969.524 E(kin)=602.793 temperature=298.709 | | Etotal =15366.731 grad(E)=67.833 E(BOND)=3551.443 E(ANGL)=1362.386 | | E(DIHE)=0.000 E(IMPR)=1396.312 E(VDW )=3342.031 E(ELEC)=-149.642 | | E(CDIH)=191.053 E(NOE )=5268.504 E(PLAN)=404.644 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69463 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69510 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69508 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69484 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.19 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69373 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69339 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=15961.496 E(kin)=621.964 temperature=308.209 | | Etotal =15339.532 grad(E)=70.218 E(BOND)=3663.332 E(ANGL)=1328.578 | | E(DIHE)=0.000 E(IMPR)=1423.510 E(VDW )=3264.493 E(ELEC)=-140.022 | | E(CDIH)=203.099 E(NOE )=5193.027 E(PLAN)=403.517 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69262 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69223 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69183 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.42 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69109 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69086 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69072 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69208 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=15926.958 E(kin)=603.328 temperature=298.974 | | Etotal =15323.630 grad(E)=68.016 E(BOND)=3523.604 E(ANGL)=1333.247 | | E(DIHE)=0.000 E(IMPR)=1416.023 E(VDW )=3372.653 E(ELEC)=-141.370 | | E(CDIH)=202.510 E(NOE )=5215.916 E(PLAN)=401.047 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69348 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69415 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.21 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69490 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69547 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69521 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69572 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=15953.324 E(kin)=606.621 temperature=300.606 | | Etotal =15346.703 grad(E)=69.526 E(BOND)=3591.795 E(ANGL)=1333.367 | | E(DIHE)=0.000 E(IMPR)=1493.379 E(VDW )=3344.769 E(ELEC)=-142.128 | | E(CDIH)=183.199 E(NOE )=5130.846 E(PLAN)=411.477 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69536 intra-atom interactions %atoms "A -1 -GUA -H21 " and "A -2 -GUA -H3' " only 1.46 A apart %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69460 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69464 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69493 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69516 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69576 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.39 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69617 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=15951.081 E(kin)=595.940 temperature=295.313 | | Etotal =15355.141 grad(E)=71.678 E(BOND)=3630.074 E(ANGL)=1352.272 | | E(DIHE)=0.000 E(IMPR)=1453.573 E(VDW )=3307.465 E(ELEC)=-147.809 | | E(CDIH)=196.574 E(NOE )=5160.112 E(PLAN)=402.880 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.38 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69656 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69738 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 69747 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69730 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69693 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.26 A apart NBONDS: found 69676 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69726 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=15945.101 E(kin)=601.208 temperature=297.924 | | Etotal =15343.894 grad(E)=67.781 E(BOND)=3637.866 E(ANGL)=1315.156 | | E(DIHE)=0.000 E(IMPR)=1466.728 E(VDW )=3297.210 E(ELEC)=-139.790 | | E(CDIH)=183.645 E(NOE )=5176.306 E(PLAN)=406.771 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69845 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69776 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69798 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69735 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69691 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.20 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69685 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=15935.578 E(kin)=625.310 temperature=309.868 | | Etotal =15310.268 grad(E)=68.444 E(BOND)=3582.459 E(ANGL)=1349.480 | | E(DIHE)=0.000 E(IMPR)=1442.645 E(VDW )=3305.784 E(ELEC)=-146.728 | | E(CDIH)=172.810 E(NOE )=5187.977 E(PLAN)=415.841 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69644 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69672 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69634 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69640 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69626 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69560 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69528 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69540 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69566 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=15941.092 E(kin)=592.211 temperature=293.466 | | Etotal =15348.880 grad(E)=72.743 E(BOND)=3691.684 E(ANGL)=1336.440 | | E(DIHE)=0.000 E(IMPR)=1487.447 E(VDW )=3291.103 E(ELEC)=-157.370 | | E(CDIH)=190.657 E(NOE )=5095.573 E(PLAN)=413.346 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69572 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69550 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69486 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69429 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69335 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69291 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69226 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.37 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69192 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=15940.998 E(kin)=600.190 temperature=297.420 | | Etotal =15340.808 grad(E)=72.597 E(BOND)=3575.684 E(ANGL)=1367.886 | | E(DIHE)=0.000 E(IMPR)=1437.830 E(VDW )=3323.412 E(ELEC)=-144.040 | | E(CDIH)=181.731 E(NOE )=5188.167 E(PLAN)=410.138 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69172 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69125 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.27 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69120 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.28 A apart NBONDS: found 69114 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.44 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69143 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69203 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69237 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=15958.349 E(kin)=613.644 temperature=304.087 | | Etotal =15344.704 grad(E)=69.604 E(BOND)=3577.635 E(ANGL)=1363.652 | | E(DIHE)=0.000 E(IMPR)=1407.991 E(VDW )=3350.003 E(ELEC)=-152.379 | | E(CDIH)=182.907 E(NOE )=5198.745 E(PLAN)=416.151 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15947.571 E(kin)=605.412 temperature=300.007 | | Etotal =15342.160 grad(E)=69.613 E(BOND)=3589.940 E(ANGL)=1328.947 | | E(DIHE)=0.000 E(IMPR)=1430.902 E(VDW )=3329.193 E(ELEC)=-145.333 | | E(CDIH)=196.130 E(NOE )=5203.524 E(PLAN)=408.856 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.112 E(kin)=13.144 temperature=6.514 | | Etotal =15.542 grad(E)=1.639 E(BOND)=39.512 E(ANGL)=25.914 | | E(DIHE)=0.000 E(IMPR)=26.006 E(VDW )=41.584 E(ELEC)=4.237 | | E(CDIH)=13.299 E(NOE )=34.228 E(PLAN)=4.375 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=15942.684 E(kin)=605.386 temperature=299.994 | | Etotal =15337.299 grad(E)=65.687 E(BOND)=3573.960 E(ANGL)=1327.539 | | E(DIHE)=0.000 E(IMPR)=1422.673 E(VDW )=3338.165 E(ELEC)=-141.499 | | E(CDIH)=197.226 E(NOE )=5209.619 E(PLAN)=409.615 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=20.329 E(kin)=13.051 temperature=6.468 | | Etotal =23.205 grad(E)=3.351 E(BOND)=39.307 E(ANGL)=26.120 | | E(DIHE)=0.000 E(IMPR)=26.804 E(VDW )=44.693 E(ELEC)=7.020 | | E(CDIH)=14.467 E(NOE )=41.247 E(PLAN)=5.447 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 69245 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.42 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69240 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.26 A apart NBONDS: found 69290 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69317 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69366 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69415 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 69409 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.44 A apart NBONDS: found 69428 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69475 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=15944.673 E(kin)=628.361 temperature=311.379 | | Etotal =15316.312 grad(E)=67.943 E(BOND)=3579.006 E(ANGL)=1320.518 | | E(DIHE)=0.000 E(IMPR)=1437.394 E(VDW )=3347.377 E(ELEC)=-144.707 | | E(CDIH)=178.317 E(NOE )=5185.287 E(PLAN)=413.121 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69510 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 69594 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 69683 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 69759 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69779 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69963 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 70006 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=15939.087 E(kin)=614.328 temperature=304.425 | | Etotal =15324.759 grad(E)=71.214 E(BOND)=3592.575 E(ANGL)=1309.110 | | E(DIHE)=0.000 E(IMPR)=1442.302 E(VDW )=3317.401 E(ELEC)=-148.709 | | E(CDIH)=202.263 E(NOE )=5199.209 E(PLAN)=410.609 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70074 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.27 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 70147 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70196 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 70180 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70152 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70136 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=15956.427 E(kin)=620.987 temperature=307.725 | | Etotal =15335.440 grad(E)=69.463 E(BOND)=3669.056 E(ANGL)=1289.765 | | E(DIHE)=0.000 E(IMPR)=1430.857 E(VDW )=3284.708 E(ELEC)=-141.260 | | E(CDIH)=181.318 E(NOE )=5211.994 E(PLAN)=409.003 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 70211 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.23 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70178 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70195 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70193 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 70231 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70228 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=15946.539 E(kin)=581.031 temperature=287.925 | | Etotal =15365.509 grad(E)=70.429 E(BOND)=3640.891 E(ANGL)=1319.519 | | E(DIHE)=0.000 E(IMPR)=1462.628 E(VDW )=3275.450 E(ELEC)=-147.716 | | E(CDIH)=199.948 E(NOE )=5205.850 E(PLAN)=408.937 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70198 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 70156 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.29 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70108 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70049 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70093 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.36 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.25 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.43 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70164 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 70285 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=15952.132 E(kin)=608.407 temperature=301.491 | | Etotal =15343.726 grad(E)=70.111 E(BOND)=3589.342 E(ANGL)=1286.233 | | E(DIHE)=0.000 E(IMPR)=1422.918 E(VDW )=3344.405 E(ELEC)=-138.191 | | E(CDIH)=213.847 E(NOE )=5219.131 E(PLAN)=406.041 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 70320 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.45 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70389 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 70512 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.24 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.35 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70557 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.48 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.41 A apart NBONDS: found 70530 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.31 A apart NBONDS: found 70496 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.33 A apart NBONDS: found 70533 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=15956.226 E(kin)=605.839 temperature=300.219 | | Etotal =15350.386 grad(E)=69.913 E(BOND)=3512.651 E(ANGL)=1341.804 | | E(DIHE)=0.000 E(IMPR)=1417.046 E(VDW )=3415.665 E(ELEC)=-145.542 | | E(CDIH)=198.385 E(NOE )=5199.375 E(PLAN)=411.002 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.40 A apart NBONDS: found 70515 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.46 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70498 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.38 A apart NBONDS: found 70391 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70352 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.28 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.49 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 70317 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.35 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.47 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.49 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 70265 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.41 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70241 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.28 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.41 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 70196 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=15966.519 E(kin)=625.505 temperature=309.964 | | Etotal =15341.015 grad(E)=69.739 E(BOND)=3578.036 E(ANGL)=1380.997 | | E(DIHE)=0.000 E(IMPR)=1457.981 E(VDW )=3377.842 E(ELEC)=-144.835 | | E(CDIH)=193.626 E(NOE )=5090.706 E(PLAN)=406.662 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.45 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 70204 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.33 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.36 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70153 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.42 A apart NBONDS: found 70136 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 70212 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.26 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.50 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 70191 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 70051 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.42 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69925 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=15948.749 E(kin)=611.540 temperature=303.044 | | Etotal =15337.209 grad(E)=71.925 E(BOND)=3589.214 E(ANGL)=1331.326 | | E(DIHE)=0.000 E(IMPR)=1404.627 E(VDW )=3341.143 E(ELEC)=-142.332 | | E(CDIH)=200.654 E(NOE )=5207.118 E(PLAN)=405.459 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69867 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.43 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.40 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.22 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69888 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.45 A apart NBONDS: found 69855 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.50 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.44 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.43 A apart NBONDS: found 69841 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.29 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.46 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.33 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.39 A apart NBONDS: found 69764 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.36 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69708 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.38 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.45 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.40 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -3 -CYT -H5 " and "A -21 -CYT -O2 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69462 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=15937.199 E(kin)=611.242 temperature=302.896 | | Etotal =15325.956 grad(E)=67.898 E(BOND)=3590.793 E(ANGL)=1291.124 | | E(DIHE)=0.000 E(IMPR)=1414.677 E(VDW )=3324.896 E(ELEC)=-153.468 | | E(CDIH)=234.137 E(NOE )=5214.327 E(PLAN)=409.469 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.48 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.25 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.37 A apart NBONDS: found 69398 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.28 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69357 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.27 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.34 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69314 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.30 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.34 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.24 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.32 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -18 -URI -H2' " and "A -19 -GUA -H8 " only 1.50 A apart %atoms "A -19 -GUA -O6 " and "A -20 -CYT -H42 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.32 A apart NBONDS: found 69272 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.32 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.26 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.41 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.26 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.25 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.34 A apart NBONDS: found 69254 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.35 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.30 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.47 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.22 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.23 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.30 A apart NBONDS: found 69199 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.33 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.33 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.46 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.35 A apart NBONDS: found 69172 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.34 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.32 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.44 A apart %atoms "A -3 -CYT -H41 " and "A -20 -CYT -O2 " only 1.50 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.47 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.31 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69140 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=15958.079 E(kin)=594.530 temperature=294.614 | | Etotal =15363.549 grad(E)=74.260 E(BOND)=3565.758 E(ANGL)=1336.599 | | E(DIHE)=0.000 E(IMPR)=1466.625 E(VDW )=3261.699 E(ELEC)=-156.628 | | E(CDIH)=227.560 E(NOE )=5247.099 E(PLAN)=414.838 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=15949.083 E(kin)=605.501 temperature=300.051 | | Etotal =15343.582 grad(E)=69.851 E(BOND)=3589.568 E(ANGL)=1332.459 | | E(DIHE)=0.000 E(IMPR)=1428.271 E(VDW )=3329.285 E(ELEC)=-146.367 | | E(CDIH)=197.241 E(NOE )=5204.360 E(PLAN)=408.765 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.702 E(kin)=12.956 temperature=6.420 | | Etotal =15.774 grad(E)=1.583 E(BOND)=37.675 E(ANGL)=24.609 | | E(DIHE)=0.000 E(IMPR)=24.216 E(VDW )=40.025 E(ELEC)=4.169 | | E(CDIH)=13.310 E(NOE )=39.282 E(PLAN)=4.642 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=15943.084 E(kin)=605.393 temperature=299.998 | | Etotal =15337.691 grad(E)=65.947 E(BOND)=3574.936 E(ANGL)=1327.847 | | E(DIHE)=0.000 E(IMPR)=1423.023 E(VDW )=3337.610 E(ELEC)=-141.803 | | E(CDIH)=197.227 E(NOE )=5209.290 E(PLAN)=409.562 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=19.893 E(kin)=13.046 temperature=6.465 | | Etotal =22.862 grad(E)=3.421 E(BOND)=39.389 E(ANGL)=26.055 | | E(DIHE)=0.000 E(IMPR)=26.684 E(VDW )=44.468 E(ELEC)=6.976 | | E(CDIH)=14.397 E(NOE )=41.147 E(PLAN)=5.404 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -0.04225 0.01807 -0.00737 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR>close refine.tra end %X-PLOR>-ERR: File refine.tra was not open. X-PLOR> X-PLOR>! Compute dynamics average over second half of trajectory. X-PLOR> X-PLOR>evaluate ($steps2=$steps/2) EVALUATE: symbol $STEPS2 set to 20000.0 (real) X-PLOR>dynamics analysis average AVECOR> input=refine.tra ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. AVECOR> begin=$steps2 AVECOR> skip=200 AVECOR> stop=$steps AVECOR>end REMARKS FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.tra" REMARKS DATE:18-Aug-96 02:21:16 created by user: READC: reading file= 1 ISTART= 200 READC: 677 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 20000 SKIP= 200 STOP= 40000 READC: TIMEstep= 0.00050000 ps header= CORD READC: complete. 101 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>close refine.tra end ! disposition=delete doesn't work X-PLOR> X-PLOR>! Final minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.30 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69365 intra-atom interactions %atoms "A -1 -GUA -H22 " and "A -3 -CYT -H5 " only 1.31 A apart %atoms "A -1 -GUA -H1 " and "A -20 -CYT -O2 " only 1.31 A apart %atoms "A -2 -GUA -H1 " and "A -4 -ADE -H61 " only 1.49 A apart %atoms "A -2 -GUA -H2' " and "A -3 -CYT -H6 " only 1.43 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -N3 " only 1.28 A apart %atoms "A -3 -CYT -H41 " and "A -21 -CYT -H42 " only 1.48 A apart %atoms "A -3 -CYT -H42 " and "A -20 -CYT -N3 " only 1.29 A apart %atoms "A -3 -CYT -H42 " and "A -21 -CYT -H42 " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -20 -CYT -N3 " and "A -21 -CYT -H42 " only 1.36 A apart NBONDS: found 69348 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =14785.498 grad(E)=15.039 E(BOND)=3410.452 E(ANGL)=1109.229 | | E(DIHE)=0.000 E(IMPR)=1358.640 E(VDW )=3325.890 E(ELEC)=-142.067 | | E(CDIH)=194.758 E(NOE )=5119.940 E(PLAN)=408.656 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =14736.551 grad(E)=6.127 E(BOND)=3373.066 E(ANGL)=1084.992 | | E(DIHE)=0.000 E(IMPR)=1355.966 E(VDW )=3336.528 E(ELEC)=-142.108 | | E(CDIH)=191.325 E(NOE )=5128.379 E(PLAN)=408.403 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =14727.055 grad(E)=3.262 E(BOND)=3376.204 E(ANGL)=1080.304 | | E(DIHE)=0.000 E(IMPR)=1355.649 E(VDW )=3321.953 E(ELEC)=-142.567 | | E(CDIH)=190.019 E(NOE )=5137.122 E(PLAN)=408.371 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =14723.750 grad(E)=1.182 E(BOND)=3376.586 E(ANGL)=1078.858 | | E(DIHE)=0.000 E(IMPR)=1354.475 E(VDW )=3319.719 E(ELEC)=-143.255 | | E(CDIH)=188.551 E(NOE )=5140.560 E(PLAN)=408.256 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =14721.994 grad(E)=1.293 E(BOND)=3374.990 E(ANGL)=1077.720 | | E(DIHE)=0.000 E(IMPR)=1353.681 E(VDW )=3320.234 E(ELEC)=-143.718 | | E(CDIH)=188.239 E(NOE )=5142.923 E(PLAN)=407.926 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =14720.722 grad(E)=1.470 E(BOND)=3375.405 E(ANGL)=1077.692 | | E(DIHE)=0.000 E(IMPR)=1353.373 E(VDW )=3320.038 E(ELEC)=-144.182 | | E(CDIH)=189.635 E(NOE )=5140.853 E(PLAN)=407.909 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =14719.453 grad(E)=1.132 E(BOND)=3376.442 E(ANGL)=1078.037 | | E(DIHE)=0.000 E(IMPR)=1352.169 E(VDW )=3318.272 E(ELEC)=-145.084 | | E(CDIH)=189.611 E(NOE )=5142.030 E(PLAN)=407.976 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =14718.582 grad(E)=0.839 E(BOND)=3375.124 E(ANGL)=1077.595 | | E(DIHE)=0.000 E(IMPR)=1351.189 E(VDW )=3321.404 E(ELEC)=-145.675 | | E(CDIH)=190.518 E(NOE )=5140.313 E(PLAN)=408.112 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the final structure. X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. (A 1 C1' |A 1 C2' ) 1.474 1.528 -0.054 9.914 3350.720 (A 1 N1 |A 1 H1 ) 1.078 1.010 0.068 6.555 1416.000 (A 2 C4' |A 2 O4' ) 1.505 1.453 0.052 6.316 2326.888 (A 2 N9 |A 2 C4 ) 1.456 1.375 0.081 11.276 1734.375 (A 2 C4 |A 2 N3 ) 1.977 1.350 0.627 889.484 2265.306 (A 2 C4 |A 2 C5 ) 1.491 1.379 0.112 28.638 2265.306 (A 2 N3 |A 2 C2 ) 1.521 1.323 0.198 68.236 1734.375 (A 2 C2 |A 2 N2 ) 1.081 1.341 -0.260 74.933 1110.000 (A 2 C2 |A 2 N1 ) 1.553 1.373 0.180 55.990 1734.375 (A 2 N2 |A 2 H22 ) 1.176 1.010 0.166 39.242 1416.000 (A 2 N1 |A 2 C6 ) 1.603 1.391 0.212 102.268 2265.306 (A 2 C6 |A 2 C5 ) 2.009 1.419 0.590 387.027 1110.000 (A 2 C2' |A 2 C3' ) 1.448 1.525 -0.077 16.524 2769.190 (A 2 C2' |A 2 H2' ) 1.014 1.090 -0.076 11.552 2000.000 (A 3 C5' |A 3 C4' ) 1.567 1.510 0.057 6.374 1982.674 (A 3 C1' |A 3 N1 ) 1.366 1.470 -0.104 25.120 2326.889 (A 3 N1 |A 3 C2 ) 1.892 1.397 0.495 271.730 1110.000 (A 3 N1 |A 3 C6 ) 1.545 1.367 0.178 98.092 3083.333 (A 3 C2 |A 3 N3 ) 1.567 1.353 0.214 79.419 1734.375 (A 3 N3 |A 3 C4 ) 1.924 1.335 0.589 784.902 2265.306 (A 3 N4 |A 3 H41 ) 0.960 1.010 -0.050 3.582 1416.000 (A 3 N4 |A 3 H42 ) 1.099 1.010 0.089 11.332 1416.000 (A 3 C4 |A 3 C5 ) 1.605 1.425 0.180 55.994 1734.375 (A 3 C5 |A 3 C6 ) 1.575 1.339 0.236 96.524 1734.375 (A 3 C5 |A 3 H5 ) 1.038 1.090 -0.052 5.337 2000.000 (A 3 C1' |A 3 H1' ) 1.035 1.090 -0.055 6.054 2000.000 (A 19 C2 |A 19 N1 ) 1.320 1.373 -0.053 4.871 1734.375 (A 19 N2 |A 19 H22 ) 1.090 1.010 0.080 9.065 1416.000 (A 19 C6 |A 19 O6 ) 1.157 1.237 -0.080 8.862 1370.370 (A 19 C6 |A 19 C5 ) 1.324 1.419 -0.095 9.924 1110.000 (A 20 N1 |A 20 C2 ) 1.324 1.397 -0.073 5.924 1110.000 (A 20 C4 |A 20 C5 ) 1.374 1.425 -0.051 4.538 1734.375 (A 21 N1 |A 21 C2 ) 1.313 1.397 -0.084 7.813 1110.000 (A 21 C2 |A 21 N3 ) 1.290 1.353 -0.063 6.781 1734.375 (A 21 C4 |A 21 N4 ) 1.264 1.335 -0.071 6.848 1370.370 (A 21 C4 |A 21 C5 ) 1.364 1.425 -0.061 6.461 1734.375 Number of violations greater 0.050: 36 RMS deviation= 0.051 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.511824E-01 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 36.0000 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 1 C4' |A 1 O4' |A 1 C1' ) 104.501 109.600 -5.099 10.755 1357.996 (A 1 C4' |A 1 C3' |A 1 O3' ) 121.065 110.500 10.565 15.133 445.032 (A 1 C1' |A 1 C2' |A 1 C3' ) 96.333 101.500 -5.167 11.044 1357.996 (A 1 C2 |A 1 N2 |A 1 H21 ) 141.365 120.000 21.365 14.601 105.000 (A 1 C2 |A 1 N2 |A 1 H22 ) 102.749 120.000 -17.251 9.519 105.000 (A 2 C5' |A 2 C4' |A 2 O4' ) 114.452 109.200 5.252 4.716 561.212 (A 2 O4' |A 2 C4' |A 2 C3' ) 100.390 105.500 -5.110 4.464 561.212 (A 2 C4' |A 2 C3' |A 2 O3' ) 124.588 110.500 14.088 26.905 445.032 (A 2 N9 |A 2 C1' |A 2 C2' ) 125.364 113.400 11.964 18.735 429.678 (A 2 C1' |A 2 N9 |A 2 C4 ) 139.025 126.500 12.525 31.104 650.874 (A 2 C1' |A 2 N9 |A 2 C8 ) 115.416 127.000 -11.584 26.607 650.874 (A 2 N9 |A 2 C4 |A 2 N3 ) 138.261 126.000 12.261 46.350 1012.199 (A 2 N3 |A 2 C4 |A 2 C5 ) 118.698 128.600 -9.902 43.530 1457.566 (A 2 C4 |A 2 N3 |A 2 C2 ) 118.553 111.900 6.653 19.655 1457.566 (A 2 C2 |A 2 N2 |A 2 H21 ) 78.479 120.000 -41.521 55.142 105.000 (A 2 C2 |A 2 N2 |A 2 H22 ) 73.213 120.000 -46.787 70.015 105.000 (A 2 C2 |A 2 N1 |A 2 H1 ) 105.588 119.300 -13.712 6.014 105.000 (A 2 H21 |A 2 N2 |A 2 H22 ) 98.563 120.000 -21.437 14.698 105.000 (A 2 H1 |A 2 N1 |A 2 C6 ) 129.093 119.300 9.793 3.067 105.000 (A 2 N1 |A 2 C6 |A 2 O6 ) 112.485 119.900 -7.415 16.953 1012.199 (A 2 C2' |A 2 C3' |A 2 O3' ) 97.835 111.000 -13.165 20.259 383.726 (A 2 C3' |A 2 C2' |A 2 O2' ) 105.873 113.300 -7.427 6.011 357.719 (A 2 C3' |A 2 C2' |A 2 H2' ) 104.586 111.410 -6.824 14.183 1000.000 (A 3 C5' |A 3 C4' |A 3 O4' ) 102.716 109.200 -6.484 7.187 561.212 (A 3 C5' |A 3 C4' |A 3 C3' ) 128.587 115.500 13.087 25.506 488.878 (A 3 C4' |A 3 C3' |A 3 O3' ) 118.583 110.500 8.083 8.856 445.032 (A 3 O4' |A 3 C1' |A 3 H1' ) 112.077 106.860 5.217 8.290 1000.000 (A 3 C1' |A 3 N1 |A 3 C2 ) 109.886 118.800 -8.914 22.002 909.071 (A 3 C1' |A 3 N1 |A 3 C6 ) 126.034 120.800 5.234 6.376 763.873 (A 3 N1 |A 3 C1' |A 3 H1' ) 100.418 107.700 -7.282 16.151 1000.000 (A 3 C1' |A 3 C2' |A 3 O2' ) 104.963 110.600 -5.637 3.463 357.719 (A 3 N1 |A 3 C2 |A 3 N3 ) 112.550 119.200 -6.650 10.017 743.656 (A 3 C4 |A 3 N4 |A 3 H42 ) 129.011 120.000 9.011 2.597 105.000 (A 3 H41 |A 3 N4 |A 3 H42 ) 107.405 120.000 -12.595 5.074 105.000 (A 3 C2' |A 3 C3' |A 3 O3' ) 101.683 111.000 -9.317 10.148 383.726 (A 3 C2' |A 3 O2' |A 3 HO2') 101.023 107.300 -6.277 1.674 139.500 (A 18 C2 |A 18 N3 |A 18 H3 ) 123.382 116.500 6.882 1.515 105.000 (A 18 H3 |A 18 N3 |A 18 C4 ) 109.514 116.500 -6.986 1.561 105.000 (A 18 C2' |A 18 C3' |A 18 O3' ) 116.071 111.000 5.071 3.006 383.726 (A 19 C4' |A 19 C3' |A 19 O3' ) 115.771 110.500 5.271 3.766 445.032 (A 19 N3 |A 19 C2 |A 19 N2 ) 125.812 119.900 5.912 7.918 743.656 (A 19 N2 |A 19 C2 |A 19 N1 ) 110.609 116.200 -5.591 4.283 449.866 (A 19 C2 |A 19 N2 |A 19 H22 ) 132.578 120.000 12.578 5.060 105.000 (A 19 C2 |A 19 N1 |A 19 H1 ) 110.169 119.300 -9.131 2.667 105.000 (A 19 H21 |A 19 N2 |A 19 H22 ) 111.042 120.000 -8.958 2.566 105.000 (A 20 C5' |A 20 C4' |A 20 C3' ) 123.482 115.500 7.982 9.488 488.878 (A 20 C4' |A 20 C3' |A 20 O3' ) 117.577 110.500 7.077 6.790 445.032 (A 21 C5' |A 21 C4' |A 21 C3' ) 120.510 115.500 5.010 3.738 488.878 (A 21 C4 |A 21 N4 |A 21 H41 ) 108.470 120.000 -11.530 4.252 105.000 (A 21 C4 |A 21 N4 |A 21 H42 ) 80.012 120.000 -39.988 51.144 105.000 Number of violations greater 5.000: 50 RMS deviation= 3.007 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 3.00728 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 50.0000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (A 1 C1' |A 1 C4 |A 1 C8 |A 1 N9 ) 10.343 0.000 -10.343 78.206 2400.000 0 (A 1 N9 |A 1 C4 |A 1 C5 |A 1 N7 ) 8.768 0.000 -8.768 5.855 250.000 0 (A 1 C5 |A 1 N7 |A 1 C8 |A 1 N9 ) -9.503 0.000 9.503 6.877 250.000 0 (A 1 N7 |A 1 C8 |A 1 N9 |A 1 C4 ) 15.030 0.000 -15.030 17.204 250.000 0 (A 1 C8 |A 1 N9 |A 1 C4 |A 1 C5 ) -13.767 0.000 13.767 14.433 250.000 0 (A 1 N1 |A 1 C6 |A 1 C5 |A 1 C4 ) -5.536 0.000 5.536 2.334 250.000 0 (A 1 C8 |A 1 C4 |A 1 C5 |A 1 N1 ) 173.002 180.000 6.998 7.422 250.000 2 (A 1 C8 |A 1 C5 |A 1 C4 |A 1 C2 ) -172.487 -180.000 -7.513 8.548 250.000 2 (A 1 N3 |A 1 C4 |A 1 C5 |A 1 N7 ) -171.410 -180.000 -8.590 11.154 250.000 2 (A 2 N3 |A 2 C2 |A 2 N2 |A 2 H21 ) 6.551 0.000 -6.551 26.142 2000.000 0 (A 2 N9 |A 2 C4 |A 2 C5 |A 2 N7 ) -6.210 0.000 6.210 2.937 250.000 0 (A 2 C4 |A 2 C5 |A 2 N7 |A 2 C8 ) 8.555 0.000 -8.555 5.573 250.000 0 (A 2 C5 |A 2 N7 |A 2 C8 |A 2 N9 ) -8.096 0.000 8.096 4.991 250.000 0 (A 2 N2 |A 2 N3 |A 2 N1 |A 2 C2 ) 14.191 0.000 -14.191 147.230 2400.000 0 (A 2 O6 |A 2 N1 |A 2 C5 |A 2 C6 ) 5.898 0.000 -5.898 25.429 2400.000 0 (A 2 C4 |A 2 N3 |A 2 C2 |A 2 N1 ) -17.875 0.000 17.875 24.331 250.000 0 (A 2 N3 |A 2 C2 |A 2 N1 |A 2 C6 ) 20.317 0.000 -20.317 31.435 250.000 0 (A 2 C2 |A 2 N1 |A 2 C6 |A 2 C5 ) -11.465 0.000 11.465 10.009 250.000 0 (A 2 C5 |A 2 C4 |A 2 N3 |A 2 C2 ) 9.073 0.000 -9.073 6.269 250.000 0 (A 2 H22 |A 2 H21 |A 2 C2 |A 2 N2 ) 56.561 0.000 -56.561 243.627 250.000 0 (A 2 H8 |A 2 N7 |A 2 N9 |A 2 C8 ) 7.545 0.000 -7.545 17.340 1000.000 0 (A 2 C8 |A 2 C5 |A 2 C4 |A 2 C2 ) -174.555 -180.000 -5.445 4.502 250.000 2 (A 2 H1' |A 2 C2' |A 2 O4' |A 2 N9 ) -59.700 -65.000 -5.300 8.556 1000.000 0 (A 3 N4 |A 3 N3 |A 3 C5 |A 3 C4 ) 6.344 0.000 -6.344 29.420 2400.000 0 (A 3 N1 |A 3 C2 |A 3 N3 |A 3 C4 ) -5.952 0.000 5.952 2.698 250.000 0 (A 3 C6 |A 3 N1 |A 3 C2 |A 3 N3 ) 6.055 0.000 -6.055 2.792 250.000 0 (A 3 H1' |A 3 C2' |A 3 O4' |A 3 N1 ) -59.447 -65.000 -5.553 9.392 1000.000 0 (A 4 N7 |A 4 C8 |A 4 N9 |A 4 C4 ) -5.219 0.000 5.219 2.074 250.000 0 (A 4 N6 |A 4 N1 |A 4 C5 |A 4 C6 ) -6.743 0.000 6.743 33.245 2400.000 0 (A 4 C4 |A 4 N3 |A 4 C2 |A 4 N1 ) 5.916 0.000 -5.916 2.666 250.000 0 (A 4 N3 |A 4 C2 |A 4 N1 |A 4 C6 ) -13.987 0.000 13.987 14.900 250.000 0 (A 4 C2 |A 4 N1 |A 4 C6 |A 4 C5 ) 13.107 0.000 -13.107 13.082 250.000 0 (A 4 N1 |A 4 C6 |A 4 C5 |A 4 C4 ) -6.293 0.000 6.293 3.016 250.000 0 (A 4 H2 |A 4 N1 |A 4 N3 |A 4 C2 ) 7.156 0.000 -7.156 15.599 1000.000 0 (A 19 N2 |A 19 N3 |A 19 N1 |A 19 C2 ) 9.626 0.000 -9.626 67.741 2400.000 0 (A 19 H1 |A 19 C2 |A 19 C6 |A 19 N1 ) 5.675 0.000 -5.675 19.621 2000.000 0 (A 19 O6 |A 19 N1 |A 19 C5 |A 19 C6 ) 6.836 0.000 -6.836 34.166 2400.000 0 (A 19 C4 |A 19 N3 |A 19 C2 |A 19 N1 ) -5.959 0.000 5.959 2.704 250.000 0 (A 19 N3 |A 19 C2 |A 19 N1 |A 19 C6 ) 12.323 0.000 -12.323 11.565 250.000 0 (A 19 C2 |A 19 N1 |A 19 C6 |A 19 C5 ) -11.976 0.000 11.976 10.923 250.000 0 (A 19 N1 |A 19 C6 |A 19 C5 |A 19 C4 ) 6.405 0.000 -6.405 3.124 250.000 0 (A 19 H22 |A 19 H21 |A 19 C2 |A 19 N2 ) 6.570 0.000 -6.570 3.287 250.000 0 (A 19 C6 |A 19 C5 |A 19 C4 |A 19 N9 ) 174.715 180.000 5.285 4.242 250.000 2 (A 20 N1 |A 20 C2 |A 20 N3 |A 20 C4 ) 8.376 0.000 -8.376 5.342 250.000 0 (A 20 N3 |A 20 C4 |A 20 C5 |A 20 C6 ) -7.502 0.000 7.502 4.286 250.000 0 (A 20 C4 |A 20 C5 |A 20 C6 |A 20 N1 ) 7.455 0.000 -7.455 4.233 250.000 0 (A 20 C6 |A 20 N1 |A 20 C2 |A 20 N3 ) -8.401 0.000 8.401 5.374 250.000 0 (A 20 H42 |A 20 C4 |A 20 H41 |A 20 N4 ) -13.811 0.000 13.811 14.526 250.000 0 (A 21 C4 |A 21 C5 |A 21 C6 |A 21 N1 ) 5.262 0.000 -5.262 2.108 250.000 0 (A 21 C5 |A 21 C6 |A 21 N1 |A 21 C2 ) -6.999 0.000 6.999 3.731 250.000 0 (A 21 H42 |A 21 C4 |A 21 H41 |A 21 N4 ) -42.538 0.000 42.538 137.799 250.000 0 (A 21 H5 |A 21 C4 |A 21 C6 |A 21 C5 ) -5.840 0.000 5.840 10.388 1000.000 0 (A 21 H6 |A 21 N1 |A 21 C5 |A 21 C6 ) 5.991 0.000 -5.991 10.934 1000.000 0 Number of violations greater 5.000: 53 RMS deviation= 4.659 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 4.65881 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 53.0000 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 1 GUA H1' set-j-atoms A 1 GUA H3' R= 3.548 NOE= 3.86 (- 0.10/+ 0.10) Delta= 0.209 E(NOE)= 4.386 ======================================== set-i-atoms A 1 GUA H1' set-j-atoms A 1 GUA H21 R= 6.092 NOE= 4.77 (- 0.10/+ 0.10) Delta= -1.218 E(NOE)= 148.414 ======================================== set-i-atoms A 1 GUA H1' set-j-atoms A 1 GUA H8 R= 3.294 NOE= 3.73 (- 0.10/+ 0.10) Delta= 0.333 E(NOE)= 11.096 ======================================== set-i-atoms A 1 GUA H1' set-j-atoms A 2 GUA H8 R= 2.935 NOE= 4.32 (- 0.10/+ 0.10) Delta= 1.284 E(NOE)= 164.902 ======================================== set-i-atoms A 1 GUA H2' set-j-atoms A 1 GUA H21 R= 4.001 NOE= 4.70 (- 0.10/+ 0.10) Delta= 0.601 E(NOE)= 36.092 ======================================== set-i-atoms A 1 GUA H2' set-j-atoms A 1 GUA H8 R= 4.480 NOE= 4.15 (- 0.10/+ 0.10) Delta= -0.231 E(NOE)= 5.352 ======================================== set-i-atoms A 1 GUA H2' set-j-atoms A 2 GUA H1' R= 4.578 NOE= 4.19 (- 0.10/+ 0.10) Delta= -0.285 E(NOE)= 8.138 ======================================== set-i-atoms A 1 GUA H2' set-j-atoms A 2 GUA H5'' R= 3.822 NOE= 4.27 (- 0.10/+ 0.10) Delta= 0.346 E(NOE)= 11.988 ======================================== set-i-atoms A 1 GUA H3' set-j-atoms A 1 GUA H8 R= 3.562 NOE= 3.20 (- 0.10/+ 0.10) Delta= -0.266 E(NOE)= 7.075 ======================================== set-i-atoms A 1 GUA H3' set-j-atoms A 2 GUA H8 R= 3.831 NOE= 3.02 (- 0.10/+ 0.10) Delta= -0.707 E(NOE)= 50.055 ======================================== set-i-atoms A 1 GUA H21 set-j-atoms A 2 GUA H1' R= 4.136 NOE= 3.25 (- 0.10/+ 0.10) Delta= -0.781 E(NOE)= 60.955 ======================================== set-i-atoms A 1 GUA H21 set-j-atoms A 2 GUA H8 R= 3.300 NOE= 4.88 (- 0.10/+ 0.10) Delta= 1.476 E(NOE)= 217.784 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 2 GUA H1' R= 4.731 NOE= 4.21 (- 0.10/+ 0.10) Delta= -0.426 E(NOE)= 18.168 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 2 GUA H21 R= 4.080 NOE= 4.77 (- 0.10/+ 0.10) Delta= 0.593 E(NOE)= 35.167 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 2 GUA H1 R= 5.321 NOE= 4.79 (- 0.10/+ 0.10) Delta= -0.431 E(NOE)= 18.536 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 21 CYT H1' R= 3.191 NOE= 4.32 (- 0.10/+ 0.10) Delta= 1.026 E(NOE)= 105.168 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 21 CYT H2' R= 5.463 NOE= 4.67 (- 0.10/+ 0.10) Delta= -0.696 E(NOE)= 48.504 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 21 CYT H42 R= 4.246 NOE= 4.57 (- 0.10/+ 0.10) Delta= 0.220 E(NOE)= 4.826 ======================================== set-i-atoms A 1 GUA H1 set-j-atoms A 21 CYT H41 R= 4.424 NOE= 4.02 (- 0.10/+ 0.10) Delta= -0.301 E(NOE)= 9.087 ======================================== set-i-atoms A 1 GUA H1 set-j-atoms A 21 CYT H42 R= 2.945 NOE= 2.48 (- 0.10/+ 0.10) Delta= -0.366 E(NOE)= 13.368 ======================================== set-i-atoms A 2 GUA H1' set-j-atoms A 2 GUA H21 R= 5.587 NOE= 4.78 (- 0.10/+ 0.10) Delta= -0.712 E(NOE)= 50.716 ======================================== set-i-atoms A 2 GUA H1' set-j-atoms A 2 GUA H8 R= 3.229 NOE= 3.73 (- 0.10/+ 0.10) Delta= 0.398 E(NOE)= 15.808 ======================================== set-i-atoms A 2 GUA H1' set-j-atoms A 3 CYT H6 R= 3.650 NOE= 4.30 (- 0.10/+ 0.10) Delta= 0.548 E(NOE)= 30.019 ======================================== set-i-atoms A 2 GUA H2' set-j-atoms A 3 CYT H1' R= 3.544 NOE= 4.19 (- 0.10/+ 0.10) Delta= 0.548 E(NOE)= 30.070 ======================================== set-i-atoms A 2 GUA H2' set-j-atoms A 3 CYT H3' R= 3.855 NOE= 4.26 (- 0.10/+ 0.10) Delta= 0.308 E(NOE)= 9.493 ======================================== set-i-atoms A 2 GUA H2' set-j-atoms A 3 CYT H4' R= 3.998 NOE= 4.44 (- 0.10/+ 0.10) Delta= 0.344 E(NOE)= 11.808 ======================================== set-i-atoms A 2 GUA H2' set-j-atoms A 3 CYT H5'' R= 3.715 NOE= 4.27 (- 0.10/+ 0.10) Delta= 0.453 E(NOE)= 20.541 ======================================== set-i-atoms A 2 GUA H3' set-j-atoms A 2 GUA H8 R= 3.624 NOE= 3.20 (- 0.10/+ 0.10) Delta= -0.328 E(NOE)= 10.770 ======================================== set-i-atoms A 2 GUA H3' set-j-atoms A 3 CYT H5' R= 4.402 NOE= 3.96 (- 0.10/+ 0.10) Delta= -0.344 E(NOE)= 11.827 ======================================== set-i-atoms A 2 GUA H3' set-j-atoms A 3 CYT H5'' R= 5.334 NOE= 4.91 (- 0.10/+ 0.10) Delta= -0.326 E(NOE)= 10.618 ======================================== set-i-atoms A 2 GUA H3' set-j-atoms A 3 CYT H5 R= 3.617 NOE= 3.31 (- 0.10/+ 0.10) Delta= -0.203 E(NOE)= 4.141 ======================================== set-i-atoms A 2 GUA H5'' set-j-atoms A 2 GUA H8 R= 4.670 NOE= 4.37 (- 0.10/+ 0.10) Delta= -0.202 E(NOE)= 4.076 ======================================== set-i-atoms A 2 GUA H21 set-j-atoms A 3 CYT H1' R= 4.713 NOE= 3.25 (- 0.10/+ 0.10) Delta= -1.358 E(NOE)= 184.306 ======================================== set-i-atoms A 2 GUA H21 set-j-atoms A 3 CYT H6 R= 3.344 NOE= 4.83 (- 0.10/+ 0.10) Delta= 1.382 E(NOE)= 191.068 ======================================== set-i-atoms A 2 GUA H21 set-j-atoms A 21 CYT H1' R= 5.438 NOE= 4.49 (- 0.10/+ 0.10) Delta= -0.845 E(NOE)= 71.346 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 3 CYT H1' R= 5.782 NOE= 4.21 (- 0.10/+ 0.10) Delta= -1.477 E(NOE)= 218.028 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 19 GUA H21 R= 5.457 NOE= 4.57 (- 0.10/+ 0.10) Delta= -0.786 E(NOE)= 61.802 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 19 GUA H22 R= 4.351 NOE= 3.56 (- 0.10/+ 0.10) Delta= -0.686 E(NOE)= 47.000 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 20 CYT H1' R= 5.317 NOE= 4.32 (- 0.10/+ 0.10) Delta= -0.900 E(NOE)= 80.951 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 20 CYT H2' R= 5.642 NOE= 4.67 (- 0.10/+ 0.10) Delta= -0.876 E(NOE)= 76.737 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 20 CYT H42 R= 4.164 NOE= 4.57 (- 0.10/+ 0.10) Delta= 0.302 E(NOE)= 9.140 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 21 CYT H1' R= 4.980 NOE= 4.37 (- 0.10/+ 0.10) Delta= -0.506 E(NOE)= 25.568 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 21 CYT H6 R= 5.651 NOE= 4.96 (- 0.10/+ 0.10) Delta= -0.590 E(NOE)= 34.808 ======================================== set-i-atoms A 2 GUA H8 set-j-atoms A 3 CYT H5 R= 4.792 NOE= 3.90 (- 0.10/+ 0.10) Delta= -0.793 E(NOE)= 62.916 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 3 CYT H41 R= 3.338 NOE= 4.35 (- 0.10/+ 0.10) Delta= 0.915 E(NOE)= 83.778 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 3 CYT H42 R= 2.302 NOE= 3.75 (- 0.10/+ 0.10) Delta= 1.346 E(NOE)= 181.198 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 19 GUA H1 R= 2.658 NOE= 3.52 (- 0.10/+ 0.10) Delta= 0.762 E(NOE)= 58.061 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 21 CYT H42 R= 2.643 NOE= 3.89 (- 0.10/+ 0.10) Delta= 1.145 E(NOE)= 131.159 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 21 CYT H5 R= 5.575 NOE= 4.40 (- 0.10/+ 0.10) Delta= -1.077 E(NOE)= 116.041 ======================================== set-i-atoms A 3 CYT H1' set-j-atoms A 4 ADE H5' R= 4.309 NOE= 4.68 (- 0.10/+ 0.10) Delta= 0.267 E(NOE)= 7.153 ======================================== set-i-atoms A 3 CYT H2' set-j-atoms A 4 ADE H1' R= 3.767 NOE= 4.19 (- 0.10/+ 0.10) Delta= 0.325 E(NOE)= 10.577 ======================================== set-i-atoms A 3 CYT H2' set-j-atoms A 4 ADE H4' R= 4.055 NOE= 4.44 (- 0.10/+ 0.10) Delta= 0.287 E(NOE)= 8.250 ======================================== set-i-atoms A 3 CYT H2' set-j-atoms A 19 GUA H22 R= 5.199 NOE= 4.67 (- 0.10/+ 0.10) Delta= -0.433 E(NOE)= 18.736 ======================================== set-i-atoms A 3 CYT H3' set-j-atoms A 3 CYT H5' R= 4.020 NOE= 3.69 (- 0.10/+ 0.10) Delta= -0.234 E(NOE)= 5.489 ======================================== set-i-atoms A 3 CYT H3' set-j-atoms A 4 ADE H5'' R= 5.228 NOE= 4.91 (- 0.10/+ 0.10) Delta= -0.220 E(NOE)= 4.829 ======================================== set-i-atoms A 3 CYT H3' set-j-atoms A 4 ADE H8 R= 3.462 NOE= 3.03 (- 0.10/+ 0.10) Delta= -0.329 E(NOE)= 10.799 ======================================== set-i-atoms A 3 CYT H5'' set-j-atoms A 3 CYT H6 R= 3.531 NOE= 4.06 (- 0.10/+ 0.10) Delta= 0.425 E(NOE)= 18.060 ======================================== set-i-atoms A 3 CYT HO2' set-j-atoms A 4 ADE H5' R= 2.618 NOE= 2.94 (- 0.10/+ 0.10) Delta= 0.223 E(NOE)= 4.972 ======================================== set-i-atoms A 3 CYT H41 set-j-atoms A 4 ADE H62 R= 5.064 NOE= 4.59 (- 0.10/+ 0.10) Delta= -0.371 E(NOE)= 13.751 ======================================== set-i-atoms A 3 CYT H41 set-j-atoms A 4 ADE H61 R= 4.117 NOE= 3.57 (- 0.10/+ 0.10) Delta= -0.451 E(NOE)= 20.349 ======================================== set-i-atoms A 3 CYT H41 set-j-atoms A 19 GUA H1 R= 4.798 NOE= 4.02 (- 0.10/+ 0.10) Delta= -0.675 E(NOE)= 45.496 ======================================== set-i-atoms A 3 CYT H41 set-j-atoms A 20 CYT H41 R= 5.181 NOE= 4.82 (- 0.10/+ 0.10) Delta= -0.264 E(NOE)= 6.970 ======================================== set-i-atoms A 3 CYT H41 set-j-atoms A 20 CYT H42 R= 4.059 NOE= 3.71 (- 0.10/+ 0.10) Delta= -0.254 E(NOE)= 6.467 ======================================== set-i-atoms A 3 CYT H42 set-j-atoms A 4 ADE H61 R= 3.336 NOE= 3.02 (- 0.10/+ 0.10) Delta= -0.211 E(NOE)= 4.451 ======================================== set-i-atoms A 3 CYT H42 set-j-atoms A 19 GUA H22 R= 3.770 NOE= 4.57 (- 0.10/+ 0.10) Delta= 0.697 E(NOE)= 48.626 ======================================== set-i-atoms A 3 CYT H42 set-j-atoms A 19 GUA H1 R= 3.360 NOE= 2.48 (- 0.10/+ 0.10) Delta= -0.781 E(NOE)= 61.037 ======================================== set-i-atoms A 3 CYT H5 set-j-atoms A 4 ADE H61 R= 5.939 NOE= 4.82 (- 0.10/+ 0.10) Delta= -1.018 E(NOE)= 103.598 ======================================== set-i-atoms A 4 ADE H1' set-j-atoms A 19 GUA H21 R= 5.417 NOE= 4.49 (- 0.10/+ 0.10) Delta= -0.823 E(NOE)= 67.783 ======================================== set-i-atoms A 4 ADE H1' set-j-atoms A 19 GUA H22 R= 3.993 NOE= 4.37 (- 0.10/+ 0.10) Delta= 0.281 E(NOE)= 7.920 ======================================== set-i-atoms A 4 ADE H62 set-j-atoms A 18 URI H3 R= 2.743 NOE= 2.40 (- 0.10/+ 0.10) Delta= -0.247 E(NOE)= 6.114 ======================================== set-i-atoms A 4 ADE H62 set-j-atoms A 19 GUA H1 R= 3.945 NOE= 4.42 (- 0.10/+ 0.10) Delta= 0.373 E(NOE)= 13.909 ======================================== set-i-atoms A 4 ADE H61 set-j-atoms A 18 URI H3 R= 4.272 NOE= 3.96 (- 0.10/+ 0.10) Delta= -0.213 E(NOE)= 4.547 ======================================== set-i-atoms A 4 ADE H2 set-j-atoms A 19 GUA H1' R= 5.852 NOE= 4.66 (- 0.10/+ 0.10) Delta= -1.094 E(NOE)= 119.630 ======================================== set-i-atoms A 18 URI H1' set-j-atoms A 19 GUA H5' R= 5.101 NOE= 4.68 (- 0.10/+ 0.10) Delta= -0.324 E(NOE)= 10.480 ======================================== set-i-atoms A 18 URI HO2' set-j-atoms A 19 GUA H4' R= 4.077 NOE= 3.52 (- 0.10/+ 0.10) Delta= -0.456 E(NOE)= 20.826 ======================================== set-i-atoms A 18 URI H6 set-j-atoms A 19 GUA H8 R= 4.432 NOE= 4.76 (- 0.10/+ 0.10) Delta= 0.229 E(NOE)= 5.263 ======================================== set-i-atoms A 19 GUA H1' set-j-atoms A 19 GUA H21 R= 4.460 NOE= 4.78 (- 0.10/+ 0.10) Delta= 0.215 E(NOE)= 4.606 ======================================== set-i-atoms A 19 GUA H1' set-j-atoms A 20 CYT H5' R= 5.027 NOE= 4.68 (- 0.10/+ 0.10) Delta= -0.249 E(NOE)= 6.218 ======================================== set-i-atoms A 19 GUA H2' set-j-atoms A 19 GUA H8 R= 3.760 NOE= 4.15 (- 0.10/+ 0.10) Delta= 0.289 E(NOE)= 8.324 ======================================== set-i-atoms A 19 GUA H3' set-j-atoms A 19 GUA H8 R= 2.783 NOE= 3.20 (- 0.10/+ 0.10) Delta= 0.313 E(NOE)= 9.807 ======================================== set-i-atoms A 19 GUA H4' set-j-atoms A 20 CYT H5' R= 4.516 NOE= 4.17 (- 0.10/+ 0.10) Delta= -0.249 E(NOE)= 6.201 ======================================== set-i-atoms A 19 GUA HO2' set-j-atoms A 20 CYT H4' R= 3.848 NOE= 3.52 (- 0.10/+ 0.10) Delta= -0.227 E(NOE)= 5.168 ======================================== set-i-atoms A 19 GUA H21 set-j-atoms A 19 GUA H1 R= 3.152 NOE= 3.48 (- 0.10/+ 0.10) Delta= 0.228 E(NOE)= 5.212 ======================================== set-i-atoms A 19 GUA H21 set-j-atoms A 20 CYT H1' R= 4.353 NOE= 3.25 (- 0.10/+ 0.10) Delta= -0.998 E(NOE)= 99.604 ======================================== set-i-atoms A 19 GUA H21 set-j-atoms A 20 CYT H6 R= 5.625 NOE= 4.83 (- 0.10/+ 0.10) Delta= -0.699 E(NOE)= 48.820 ======================================== set-i-atoms A 19 GUA H22 set-j-atoms A 20 CYT H1' R= 5.109 NOE= 4.21 (- 0.10/+ 0.10) Delta= -0.804 E(NOE)= 64.721 ======================================== set-i-atoms A 19 GUA H8 set-j-atoms A 20 CYT H5 R= 3.185 NOE= 3.90 (- 0.10/+ 0.10) Delta= 0.614 E(NOE)= 37.734 ======================================== set-i-atoms A 19 GUA H1 set-j-atoms A 20 CYT H41 R= 4.682 NOE= 4.35 (- 0.10/+ 0.10) Delta= -0.229 E(NOE)= 5.245 ======================================== set-i-atoms A 19 GUA H1 set-j-atoms A 20 CYT H5 R= 5.722 NOE= 4.95 (- 0.10/+ 0.10) Delta= -0.672 E(NOE)= 45.190 ======================================== set-i-atoms A 20 CYT H3' set-j-atoms A 20 CYT H5'' R= 3.400 NOE= 3.08 (- 0.10/+ 0.10) Delta= -0.215 E(NOE)= 4.613 ======================================== set-i-atoms A 20 CYT H3' set-j-atoms A 20 CYT H5 R= 4.432 NOE= 4.77 (- 0.10/+ 0.10) Delta= 0.237 E(NOE)= 5.618 ======================================== set-i-atoms A 20 CYT H42 set-j-atoms A 21 CYT H42 R= 2.710 NOE= 3.26 (- 0.10/+ 0.10) Delta= 0.454 E(NOE)= 20.609 ======================================== set-i-atoms A 20 CYT H6 set-j-atoms A 21 CYT H5 R= 4.383 NOE= 4.00 (- 0.10/+ 0.10) Delta= -0.282 E(NOE)= 7.943 ======================================== set-i-atoms A 21 CYT H2' set-j-atoms A 21 CYT H6 R= 3.620 NOE= 4.00 (- 0.10/+ 0.10) Delta= 0.279 E(NOE)= 7.772 ======================================== set-i-atoms A 21 CYT H41 set-j-atoms A 21 CYT H6 R= 4.333 NOE= 4.65 (- 0.10/+ 0.10) Delta= 0.217 E(NOE)= 4.710 ======================================== set-i-atoms A 21 CYT H42 set-j-atoms A 21 CYT H5 R= 3.000 NOE= 3.71 (- 0.10/+ 0.10) Delta= 0.608 E(NOE)= 36.945 ======================================== set-i-atoms A 12 URI H4' set-j-atoms A 13 ADE H8 R= 2.790 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.210 E(NOE)= 4.396 ======================================== set-i-atoms A 12 URI H1' set-j-atoms A 13 ADE H8 R= 5.282 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.282 E(NOE)= 7.944 ======================================== set-i-atoms A 1 GUA O6 set-j-atoms A 21 CYT H42 R= 3.724 NOE= 1.90 (- 0.10/+ 0.10) Delta= -1.724 E(NOE)= 297.350 ======================================== set-i-atoms A 1 GUA H1 set-j-atoms A 21 CYT N3 R= 3.028 NOE= 1.94 (- 0.10/+ 0.10) Delta= -0.988 E(NOE)= 97.652 ======================================== set-i-atoms A 1 GUA H22 set-j-atoms A 21 CYT O2 R= 2.550 NOE= 1.90 (- 0.10/+ 0.10) Delta= -0.550 E(NOE)= 30.274 ======================================== set-i-atoms A 2 GUA O6 set-j-atoms A 20 CYT H42 R= 2.650 NOE= 1.90 (- 0.10/+ 0.10) Delta= -0.650 E(NOE)= 42.272 ======================================== set-i-atoms A 2 GUA H1 set-j-atoms A 20 CYT N3 R= 3.201 NOE= 1.94 (- 0.10/+ 0.10) Delta= -1.161 E(NOE)= 134.774 ======================================== set-i-atoms A 2 GUA H22 set-j-atoms A 20 CYT O2 R= 3.313 NOE= 1.90 (- 0.10/+ 0.10) Delta= -1.313 E(NOE)= 172.303 ======================================== set-i-atoms A 3 CYT H42 set-j-atoms A 19 GUA O6 R= 3.269 NOE= 1.90 (- 0.10/+ 0.10) Delta= -1.269 E(NOE)= 161.034 ======================================== set-i-atoms A 3 CYT N3 set-j-atoms A 19 GUA H1 R= 2.494 NOE= 1.94 (- 0.10/+ 0.10) Delta= -0.454 E(NOE)= 20.640 ======================================== set-i-atoms A 3 CYT O2 set-j-atoms A 19 GUA H22 R= 2.669 NOE= 1.90 (- 0.10/+ 0.10) Delta= -0.669 E(NOE)= 44.810 ======================================== set-i-atoms A 4 ADE N1 set-j-atoms A 18 URI H3 R= 2.198 NOE= 1.81 (- 0.10/+ 0.10) Delta= -0.288 E(NOE)= 8.275 NOEPRI: RMS diff. = 0.235, #(violat.> 0.2)= 108 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.235, #(viol.> 0.2)= 108 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.235354 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 108.000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 ======================================== A 1 GUA O4' A 1 GUA C1' A 1 GUA N9 A 1 GUA C4 Dihedral= 165.941 Energy= 0.135 C= 1.000 Equil= -158.000 Delta= 21.059 Range= 15.000 Exponent= 2 ======================================== A 2 GUA C4' A 2 GUA C3' A 2 GUA O3' A 3 CYT P Dihedral= -179.213 Energy= 0.038 C= 1.000 Equil= -153.000 Delta= 11.213 Range= 15.000 Exponent= 2 ======================================== A 2 GUA O4' A 2 GUA C1' A 2 GUA N9 A 2 GUA C4 Dihedral= 179.816 Energy= 0.016 C= 1.000 Equil= -158.000 Delta= 7.184 Range= 15.000 Exponent= 2 ======================================== A 3 CYT P A 3 CYT O5' A 3 CYT C5' A 3 CYT C4' Dihedral= 157.096 Energy= 0.011 C= 1.000 Equil= 178.000 Delta= 5.904 Range= 15.000 Exponent= 2 ======================================== A 3 CYT C4' A 3 CYT C3' A 3 CYT O3' A 4 ADE P Dihedral= -173.658 Energy= 0.010 C= 1.000 Equil= -153.000 Delta= 5.658 Range= 15.000 Exponent= 2 ======================================== A 21 CYT O4' A 21 CYT C1' A 21 CYT N1 A 21 CYT C2 Dihedral= -137.247 Energy= 0.010 C= 1.000 Equil= -158.000 Delta= -5.753 Range= 15.000 Exponent= 2 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 6 RMS deviation= 1.962 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 1.96244 (real) X-PLOR>evaluate ($v_cdih=$violations) EVALUATE: symbol $V_CDIH set to 6.00000 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 3375.12, angle 1077.59, dihedral 0, improper 1351.19, NOE 5140.31, c-dihedral 190.518, planar 408.112, VdW 3321.4, elec -145.675, total 14718.6 RMSD: bond 5.118243E-02, angle 3.00728, dihedral 0, improper 4.65881, NOE 0.235354, c-dihedral 1.96244 Violations: bond 36, angle 50, dihedral 0, improper 53, NOE 108, c-dihedral 6 X-PLOR> X-PLOR>write coordinates output=refine.pdb end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 138516 current use= 0 X-PLOR: total CPU time= 3006.9067 s X-PLOR: entry time at 02:20:42 18-Aug-96 X-PLOR: exit time at 03:11:13 18-Aug-96