X-PLOR: V3.834 user: on: Alpha/OSF at: 27-Apr-96 13:39:07 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! make-template.inp -- Build extended structure for local geometry reference X-PLOR>! Dave Schweisguth , 27 Apr 1996 X-PLOR>! Derived from nmr/generate_template.inp X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use xplor -s ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/xplor.seed opened. SEED=121947.41217041 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) X-PLOR> X-PLOR>vector ident (x) (all) ! Set X coordinate to atom number(!) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (x=x/10) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (y=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (z=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (fbeta=50) (all) ! Friction coefficient, in 1/ps SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (mass=100) (all) ! Heavy masses, in amu SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=5.5 NBDSET> rconst=20 NBDSET> nbxmod=-2 NBDSET> repel=0.9 ! Repulsive non-bonded energy only NBDSET> wmin=0.1 NBDSET> tolerance=1 NBDSET> rexp=2 ! default NBDSET> irexp=2 ! default NBDSET> inhibit=0.25 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! Parameter set may or may not contain dihedral energies X-PLOR> X-PLOR>flags exclude * include bond angle dihe vdw end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 34334 intra-atom interactions NBONDS: found 33020 intra-atom interactions %atoms "A -16 -CYT -O1P " and "A -16 -CYT -N1 " only 0.09 A apart NBONDS: found 28571 intra-atom interactions NBONDS: found 30046 intra-atom interactions NBONDS: found 29895 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =0.45E+07 grad(E)=2705.596 E(BOND)=0.12E+07 E(ANGL)=599632.416 | | E(DIHE)=0.000 E(VDW )=0.28E+07 | ------------------------------------------------------------------------------- NBONDS: found 28320 intra-atom interactions NBONDS: found 25941 intra-atom interactions NBONDS: found 24660 intra-atom interactions NBONDS: found 22226 intra-atom interactions NBONDS: found 21364 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =0.19E+07 grad(E)=1668.559 E(BOND)=606904.811 E(ANGL)=297011.369 | | E(DIHE)=0.000 E(VDW )=956392.672 | ------------------------------------------------------------------------------- NBONDS: found 19816 intra-atom interactions NBONDS: found 19389 intra-atom interactions NBONDS: found 18918 intra-atom interactions NBONDS: found 18050 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =0.10E+07 grad(E)=901.061 E(BOND)=309304.641 E(ANGL)=162648.850 | | E(DIHE)=0.000 E(VDW )=541651.736 | ------------------------------------------------------------------------------- NBONDS: found 17587 intra-atom interactions NBONDS: found 17092 intra-atom interactions NBONDS: found 16536 intra-atom interactions NBONDS: found 15846 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0000 ----------------------- | Etotal =664847.442 grad(E)=657.070 E(BOND)=215024.056 E(ANGL)=115527.496 | | E(DIHE)=0.000 E(VDW )=334295.890 | ------------------------------------------------------------------------------- NBONDS: found 15292 intra-atom interactions NBONDS: found 14639 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =483366.339 grad(E)=512.334 E(BOND)=172756.750 E(ANGL)=91529.724 | | E(DIHE)=0.000 E(VDW )=219079.865 | ------------------------------------------------------------------------------- NBONDS: found 14126 intra-atom interactions NBONDS: found 13796 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =360409.635 grad(E)=439.545 E(BOND)=136007.345 E(ANGL)=62781.449 | | E(DIHE)=0.000 E(VDW )=161620.841 | ------------------------------------------------------------------------------- NBONDS: found 13313 intra-atom interactions NBONDS: found 12935 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =286139.511 grad(E)=292.948 E(BOND)=109860.199 E(ANGL)=42633.771 | | E(DIHE)=0.000 E(VDW )=133645.541 | ------------------------------------------------------------------------------- NBONDS: found 12538 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =252842.047 grad(E)=220.656 E(BOND)=102311.707 E(ANGL)=32684.130 | | E(DIHE)=0.000 E(VDW )=117846.211 | ------------------------------------------------------------------------------- NBONDS: found 12219 intra-atom interactions NBONDS: found 12022 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =230125.644 grad(E)=172.635 E(BOND)=98594.276 E(ANGL)=29155.213 | | E(DIHE)=0.000 E(VDW )=102376.155 | ------------------------------------------------------------------------------- NBONDS: found 11803 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =215111.655 grad(E)=146.796 E(BOND)=93894.872 E(ANGL)=25628.130 | | E(DIHE)=0.000 E(VDW )=95588.653 | ------------------------------------------------------------------------------- NBONDS: found 11608 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =204664.179 grad(E)=134.013 E(BOND)=91608.002 E(ANGL)=22270.492 | | E(DIHE)=0.000 E(VDW )=90785.685 | ------------------------------------------------------------------------------- NBONDS: found 11396 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =194154.205 grad(E)=139.198 E(BOND)=91272.926 E(ANGL)=18115.998 | | E(DIHE)=0.000 E(VDW )=84765.281 | ------------------------------------------------------------------------------- NBONDS: found 11152 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =186261.127 grad(E)=119.746 E(BOND)=89711.537 E(ANGL)=15733.804 | | E(DIHE)=0.000 E(VDW )=80815.786 | ------------------------------------------------------------------------------- NBONDS: found 10832 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =179053.576 grad(E)=103.361 E(BOND)=86491.392 E(ANGL)=12603.249 | | E(DIHE)=0.000 E(VDW )=79958.935 | ------------------------------------------------------------------------------- NBONDS: found 10574 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =174044.518 grad(E)=87.343 E(BOND)=87175.560 E(ANGL)=11656.888 | | E(DIHE)=0.000 E(VDW )=75212.069 | ------------------------------------------------------------------------------- NBONDS: found 10341 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =169768.014 grad(E)=76.281 E(BOND)=83256.863 E(ANGL)=10022.813 | | E(DIHE)=0.000 E(VDW )=76488.338 | ------------------------------------------------------------------------------- NBONDS: found 10090 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =166762.323 grad(E)=63.894 E(BOND)=84439.971 E(ANGL)=9481.105 | | E(DIHE)=0.000 E(VDW )=72841.247 | ------------------------------------------------------------------------------- NBONDS: found 9834 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =164839.829 grad(E)=51.418 E(BOND)=83390.316 E(ANGL)=8489.307 | | E(DIHE)=0.000 E(VDW )=72960.206 | ------------------------------------------------------------------------------- NBONDS: found 9630 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0000 ----------------------- | Etotal =163332.841 grad(E)=49.198 E(BOND)=83641.461 E(ANGL)=8020.332 | | E(DIHE)=0.000 E(VDW )=71671.047 | ------------------------------------------------------------------------------- NBONDS: found 9342 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =162147.858 grad(E)=39.563 E(BOND)=82816.391 E(ANGL)=7617.077 | | E(DIHE)=0.000 E(VDW )=71714.390 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>flags include impr end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODIMP: improper type-based parameters retrieved NBONDS: found 9266 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =389492.053 grad(E)=373.989 E(BOND)=86817.513 E(ANGL)=31758.333 | | E(DIHE)=0.000 E(IMPR)=192556.915 E(VDW )=78359.292 | ------------------------------------------------------------------------------- --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =368457.734 grad(E)=179.670 E(BOND)=81004.912 E(ANGL)=44432.819 | | E(DIHE)=0.000 E(IMPR)=159104.268 E(VDW )=83915.736 | ------------------------------------------------------------------------------- NBONDS: found 9174 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =360850.444 grad(E)=135.216 E(BOND)=84944.865 E(ANGL)=48415.580 | | E(DIHE)=0.000 E(IMPR)=143980.763 E(VDW )=83509.236 | ------------------------------------------------------------------------------- NBONDS: found 9095 intra-atom interactions NBONDS: found 9016 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =345593.883 grad(E)=247.481 E(BOND)=97594.196 E(ANGL)=51110.554 | | E(DIHE)=0.000 E(IMPR)=114758.765 E(VDW )=82130.368 | ------------------------------------------------------------------------------- NBONDS: found 8971 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =319796.898 grad(E)=308.357 E(BOND)=92899.422 E(ANGL)=49774.777 | | E(DIHE)=0.000 E(IMPR)=93099.338 E(VDW )=84023.361 | ------------------------------------------------------------------------------- NBONDS: found 8987 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =316770.057 grad(E)=286.867 E(BOND)=91759.131 E(ANGL)=49512.080 | | E(DIHE)=0.000 E(IMPR)=91376.668 E(VDW )=84122.178 | ------------------------------------------------------------------------------- --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =316506.749 grad(E)=273.793 E(BOND)=91682.305 E(ANGL)=49472.589 | | E(DIHE)=0.000 E(IMPR)=91234.771 E(VDW )=84117.085 | ------------------------------------------------------------------------------- --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =316506.729 grad(E)=273.792 E(BOND)=91682.299 E(ANGL)=49472.586 | | E(DIHE)=0.000 E(IMPR)=91234.760 E(VDW )=84117.084 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =319515.473 grad(E)=537.438 E(BOND)=91682.298 E(ANGL)=49472.586 | | E(DIHE)=0.000 E(IMPR)=94243.505 E(VDW )=84117.084 | ------------------------------------------------------------------------------- %POWELL-ERR: Line search abandoned POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=200 DYNAmics> timestep=0.001 ! default DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=50 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 0.115420349E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 velocity [A/ps] : -0.00547 0.02051 -0.12917 ang. mom. [amu A/ps] : -15597.51413 97673.57960 19816.20719 kin. ener. [Kcal/mol] : 1.38627 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 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)=317104.991 E(kin)=598.264 temperature=296.465 | | Etotal =316506.727 grad(E)=273.792 E(BOND)=91682.298 E(ANGL)=49472.586 | | E(DIHE)=0.000 E(IMPR)=91234.759 E(VDW )=84117.084 | ------------------------------------------------------------------------------- NBONDS: found 8982 intra-atom interactions NBONDS: found 8949 intra-atom interactions NBONDS: found 8946 intra-atom interactions --------------- step= 50 at 0.05000 ps -------------------------------- | E(kin)+E(total)=286738.850 E(kin)=7573.933 temperature=3753.202 | | Etotal =279164.916 grad(E)=167.671 E(BOND)=87197.960 E(ANGL)=36463.258 | | E(DIHE)=0.000 E(IMPR)=73502.985 E(VDW )=82000.713 | ------------------------------------------------------------------------------- NBONDS: found 8955 intra-atom interactions NBONDS: found 8899 intra-atom interactions NBONDS: found 8870 intra-atom interactions --------------- step= 100 at 0.10000 ps -------------------------------- | E(kin)+E(total)=257366.437 E(kin)=5289.641 temperature=2621.239 | | Etotal =252076.796 grad(E)=120.620 E(BOND)=85988.472 E(ANGL)=26687.714 | | E(DIHE)=0.000 E(IMPR)=58020.161 E(VDW )=81380.449 | ------------------------------------------------------------------------------- NBONDS: found 8842 intra-atom interactions NBONDS: found 8808 intra-atom interactions NBONDS: found 8760 intra-atom interactions --------------- step= 150 at 0.15000 ps -------------------------------- | E(kin)+E(total)=237448.316 E(kin)=3056.507 temperature=1514.628 | | Etotal =234391.809 grad(E)=78.475 E(BOND)=83475.881 E(ANGL)=21022.156 | | E(DIHE)=0.000 E(IMPR)=50213.861 E(VDW )=79679.910 | ------------------------------------------------------------------------------- NBONDS: found 8722 intra-atom interactions NBONDS: found 8727 intra-atom interactions --------------- step= 200 at 0.20000 ps -------------------------------- | E(kin)+E(total)=228044.408 E(kin)=2630.470 temperature=1303.508 | | Etotal =225413.939 grad(E)=70.861 E(BOND)=84864.336 E(ANGL)=19967.561 | | E(DIHE)=0.000 E(IMPR)=43080.643 E(VDW )=77501.399 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 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> X-PLOR>parameter PARRDR> nbonds NBDSET> rconst=2 NBDSET> nbxmod=-3 NBDSET> repel=0.75 ! Repulsive non-bonded energy only NBDSET> end PARRDR>end X-PLOR> X-PLOR>minimize powell nstep=400 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=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 7427 intra-atom interactions NBONDS: found 7864 intra-atom interactions NBONDS: found 8302 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =50579.394 grad(E)=266.825 E(BOND)=8357.321 E(ANGL)=23991.695 | | E(DIHE)=0.000 E(IMPR)=18071.015 E(VDW )=159.363 | ------------------------------------------------------------------------------- NBONDS: found 8678 intra-atom interactions NBONDS: found 8977 intra-atom interactions NBONDS: found 9134 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =16451.114 grad(E)=162.875 E(BOND)=1924.499 E(ANGL)=10198.770 | | E(DIHE)=0.000 E(IMPR)=3991.481 E(VDW )=336.364 | ------------------------------------------------------------------------------- NBONDS: found 9269 intra-atom interactions NBONDS: found 9275 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =6233.590 grad(E)=89.678 E(BOND)=720.910 E(ANGL)=3954.988 | | E(DIHE)=0.000 E(IMPR)=1345.920 E(VDW )=211.772 | ------------------------------------------------------------------------------- NBONDS: found 9313 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =4011.833 grad(E)=44.522 E(BOND)=268.904 E(ANGL)=2538.243 | | E(DIHE)=0.000 E(IMPR)=989.093 E(VDW )=215.593 | ------------------------------------------------------------------------------- NBONDS: found 9396 intra-atom interactions --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =2320.752 grad(E)=47.514 E(BOND)=253.284 E(ANGL)=1363.422 | | E(DIHE)=0.000 E(IMPR)=473.582 E(VDW )=230.464 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =1368.192 grad(E)=28.532 E(BOND)=120.824 E(ANGL)=821.326 | | E(DIHE)=0.000 E(IMPR)=167.616 E(VDW )=258.426 | ------------------------------------------------------------------------------- NBONDS: found 9553 intra-atom interactions --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =914.343 grad(E)=21.449 E(BOND)=69.885 E(ANGL)=504.528 | | E(DIHE)=0.000 E(IMPR)=91.806 E(VDW )=248.124 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =717.212 grad(E)=11.933 E(BOND)=48.641 E(ANGL)=352.573 | | E(DIHE)=0.000 E(IMPR)=84.070 E(VDW )=231.928 | ------------------------------------------------------------------------------- --------------- cycle= 225 ------ stepsize= 0.0001 ----------------------- | Etotal =579.267 grad(E)=10.413 E(BOND)=34.054 E(ANGL)=274.774 | | E(DIHE)=0.000 E(IMPR)=73.603 E(VDW )=196.836 | ------------------------------------------------------------------------------- NBONDS: found 9665 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =473.199 grad(E)=8.842 E(BOND)=31.738 E(ANGL)=248.143 | | E(DIHE)=0.000 E(IMPR)=42.497 E(VDW )=150.821 | ------------------------------------------------------------------------------- --------------- cycle= 275 ------ stepsize= 0.0001 ----------------------- | Etotal =408.651 grad(E)=7.960 E(BOND)=29.118 E(ANGL)=221.992 | | E(DIHE)=0.000 E(IMPR)=31.150 E(VDW )=126.390 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =362.071 grad(E)=6.747 E(BOND)=24.738 E(ANGL)=194.832 | | E(DIHE)=0.000 E(IMPR)=25.344 E(VDW )=117.158 | ------------------------------------------------------------------------------- --------------- cycle= 325 ------ stepsize= 0.0001 ----------------------- | Etotal =318.770 grad(E)=4.944 E(BOND)=18.782 E(ANGL)=175.125 | | E(DIHE)=0.000 E(IMPR)=20.385 E(VDW )=104.478 | ------------------------------------------------------------------------------- --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =293.874 grad(E)=4.620 E(BOND)=17.074 E(ANGL)=163.540 | | E(DIHE)=0.000 E(IMPR)=20.639 E(VDW )=92.623 | ------------------------------------------------------------------------------- --------------- cycle= 375 ------ stepsize= 0.0001 ----------------------- | Etotal =274.730 grad(E)=5.350 E(BOND)=15.686 E(ANGL)=156.046 | | E(DIHE)=0.000 E(IMPR)=19.811 E(VDW )=83.188 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =262.038 grad(E)=4.188 E(BOND)=16.308 E(ANGL)=151.173 | | E(DIHE)=0.000 E(IMPR)=18.761 E(VDW )=75.797 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=1000 DYNAmics> timestep=0.005 DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=100 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 74557590.4 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 velocity [A/ps] : 0.00682 0.10793 -0.04579 ang. mom. [amu A/ps] : 8777.30196-141213.65485 -34138.02197 kin. ener. [Kcal/mol] : 1.11574 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 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)=849.460 E(kin)=587.421 temperature=291.092 | | Etotal =262.038 grad(E)=4.188 E(BOND)=16.308 E(ANGL)=151.173 | | E(DIHE)=0.000 E(IMPR)=18.761 E(VDW )=75.797 | ------------------------------------------------------------------------------- NBONDS: found 9647 intra-atom interactions --------------- step= 100 at 0.50000 ps -------------------------------- | E(kin)+E(total)=16423.242 E(kin)=2172.892 temperature=1076.759 | | Etotal =14250.350 grad(E)=598.057 E(BOND)=2014.699 E(ANGL)=2205.089 | | E(DIHE)=0.000 E(IMPR)=9964.718 E(VDW )=65.843 | ------------------------------------------------------------------------------- --------------- step= 200 at 1.00000 ps -------------------------------- | E(kin)+E(total)=14599.473 E(kin)=2378.676 temperature=1178.734 | | Etotal =12220.798 grad(E)=555.426 E(BOND)=1481.611 E(ANGL)=2034.582 | | E(DIHE)=0.000 E(IMPR)=8641.736 E(VDW )=62.869 | ------------------------------------------------------------------------------- --------------- step= 300 at 1.50000 ps -------------------------------- | E(kin)+E(total)=14836.125 E(kin)=2124.976 temperature=1053.015 | | Etotal =12711.149 grad(E)=571.109 E(BOND)=1309.492 E(ANGL)=1787.232 | | E(DIHE)=0.000 E(IMPR)=9556.405 E(VDW )=58.019 | ------------------------------------------------------------------------------- --------------- step= 400 at 2.00000 ps -------------------------------- | E(kin)+E(total)=14463.320 E(kin)=2187.800 temperature=1084.147 | | Etotal =12275.520 grad(E)=564.795 E(BOND)=1105.694 E(ANGL)=1868.477 | | E(DIHE)=0.000 E(IMPR)=9247.200 E(VDW )=54.148 | ------------------------------------------------------------------------------- --------------- step= 500 at 2.50000 ps -------------------------------- | E(kin)+E(total)=14059.465 E(kin)=2860.033 temperature=1417.266 | | Etotal =11199.432 grad(E)=532.658 E(BOND)=1170.108 E(ANGL)=1838.549 | | E(DIHE)=0.000 E(IMPR)=8137.722 E(VDW )=53.053 | ------------------------------------------------------------------------------- --------------- step= 600 at 3.00000 ps -------------------------------- | E(kin)+E(total)=11489.190 E(kin)=2357.813 temperature=1168.395 | | Etotal =9131.377 grad(E)=459.781 E(BOND)=1359.002 E(ANGL)=2132.356 | | E(DIHE)=0.000 E(IMPR)=5590.907 E(VDW )=49.112 | ------------------------------------------------------------------------------- --------------- step= 700 at 3.50000 ps -------------------------------- | E(kin)+E(total)=10995.299 E(kin)=1742.631 temperature=863.547 | | Etotal =9252.668 grad(E)=488.019 E(BOND)=958.189 E(ANGL)=1620.056 | | E(DIHE)=0.000 E(IMPR)=6624.599 E(VDW )=49.824 | ------------------------------------------------------------------------------- --------------- step= 800 at 4.00000 ps -------------------------------- | E(kin)+E(total)=18846.821 E(kin)=2887.252 temperature=1430.755 | | Etotal =15959.569 grad(E)=632.039 E(BOND)=1890.256 E(ANGL)=2017.145 | | E(DIHE)=0.000 E(IMPR)=12003.222 E(VDW )=48.948 | ------------------------------------------------------------------------------- --------------- step= 900 at 4.50000 ps -------------------------------- | E(kin)+E(total)=16315.705 E(kin)=2300.497 temperature=1139.993 | | Etotal =14015.208 grad(E)=611.119 E(BOND)=1287.792 E(ANGL)=1780.541 | | E(DIHE)=0.000 E(IMPR)=10902.171 E(VDW )=44.704 | ------------------------------------------------------------------------------- NBONDS: found 9660 intra-atom interactions --------------- step= 1000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=15563.077 E(kin)=1916.563 temperature=949.737 | | Etotal =13646.515 grad(E)=603.325 E(BOND)=1312.032 E(ANGL)=1837.502 | | E(DIHE)=0.000 E(IMPR)=10455.382 E(VDW )=41.598 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.49365 0.49347 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> X-PLOR>! H-building won't actually place protons, since we're using a fully protonated X-PLOR>! topology/parameter set, but it may improve their positions X-PLOR>! We're using "nbonds repel", so the "elec" flag is irrelevant X-PLOR> X-PLOR>flags exclude vdw end X-PLOR>vector do (mass=1) (name h*) SELRPN: 230 atoms have been selected out of 677 X-PLOR>hbuild selection=(name h*) phistep=360 end SELRPN: 230 atoms have been selected out of 677 HBUILD: dihedral PHI STePs for spin = 360.0000 HBUILD: cutoff during water acceptor search = 7.5000 HBUILD: H5' ,H5'', placed for donor A 1 GUA C5' . HBUILD: H4' , , placed for donor A 1 GUA C4' . HBUILD: H1' , , placed for donor A 1 GUA C1' . HBUILD: H1 , , placed for donor A 1 GUA N1 . HBUILD: H8 , , placed for donor A 1 GUA C8 . HBUILD: H2' , , placed for donor A 1 GUA C2' . HBUILD: H3' , , placed for donor A 1 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 2 GUA C5' . HBUILD: H4' , , placed for donor A 2 GUA C4' . HBUILD: H1' , , placed for donor A 2 GUA C1' . HBUILD: H1 , , placed for donor A 2 GUA N1 . HBUILD: H8 , , placed for donor A 2 GUA C8 . HBUILD: H2' , , placed for donor A 2 GUA C2' . HBUILD: H3' , , placed for donor A 2 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 3 CYT C5' . HBUILD: H4' , , placed for donor A 3 CYT C4' . HBUILD: H1' , , placed for donor A 3 CYT C1' . HBUILD: H6 , , placed for donor A 3 CYT C6 . HBUILD: H5 , , placed for donor A 3 CYT C5 . HBUILD: H2' , , placed for donor A 3 CYT C2' . HBUILD: H3' , , placed for donor A 3 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 4 ADE C5' . HBUILD: H4' , , placed for donor A 4 ADE C4' . HBUILD: H1' , , placed for donor A 4 ADE C1' . HBUILD: H2 , , placed for donor A 4 ADE C2 . HBUILD: H8 , , placed for donor A 4 ADE C8 . HBUILD: H2' , , placed for donor A 4 ADE C2' . HBUILD: H3' , , placed for donor A 4 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 5 GUA C5' . HBUILD: H4' , , placed for donor A 5 GUA C4' . HBUILD: H1' , , placed for donor A 5 GUA C1' . HBUILD: H1 , , placed for donor A 5 GUA N1 . HBUILD: H8 , , placed for donor A 5 GUA C8 . HBUILD: H2' , , placed for donor A 5 GUA C2' . HBUILD: H3' , , placed for donor A 5 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 6 GUA C5' . HBUILD: H4' , , placed for donor A 6 GUA C4' . HBUILD: H1' , , placed for donor A 6 GUA C1' . HBUILD: H1 , , placed for donor A 6 GUA N1 . HBUILD: H8 , , placed for donor A 6 GUA C8 . HBUILD: H2' , , placed for donor A 6 GUA C2' . HBUILD: H3' , , placed for donor A 6 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 7 GUA C5' . HBUILD: H4' , , placed for donor A 7 GUA C4' . HBUILD: H1' , , placed for donor A 7 GUA C1' . HBUILD: H1 , , placed for donor A 7 GUA N1 . HBUILD: H8 , , placed for donor A 7 GUA C8 . HBUILD: H2' , , placed for donor A 7 GUA C2' . HBUILD: H3' , , placed for donor A 7 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 8 CYT C5' . HBUILD: H4' , , placed for donor A 8 CYT C4' . HBUILD: H1' , , placed for donor A 8 CYT C1' . HBUILD: H6 , , placed for donor A 8 CYT C6 . HBUILD: H5 , , placed for donor A 8 CYT C5 . HBUILD: H2' , , placed for donor A 8 CYT C2' . HBUILD: H3' , , placed for donor A 8 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 9 URI C5' . HBUILD: H4' , , placed for donor A 9 URI C4' . HBUILD: H1' , , placed for donor A 9 URI C1' . HBUILD: H6 , , placed for donor A 9 URI C6 . HBUILD: H3 , , placed for donor A 9 URI N3 . HBUILD: H5 , , placed for donor A 9 URI C5 . HBUILD: H2' , , placed for donor A 9 URI C2' . HBUILD: H3' , , placed for donor A 9 URI C3' . HBUILD: H5' ,H5'', placed for donor A 10 CYT C5' . HBUILD: H4' , , placed for donor A 10 CYT C4' . HBUILD: H1' , , placed for donor A 10 CYT C1' . HBUILD: H6 , , placed for donor A 10 CYT C6 . HBUILD: H5 , , placed for donor A 10 CYT C5 . HBUILD: H2' , , placed for donor A 10 CYT C2' . HBUILD: H3' , , placed for donor A 10 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 11 ADE C5' . HBUILD: H4' , , placed for donor A 11 ADE C4' . HBUILD: H1' , , placed for donor A 11 ADE C1' . HBUILD: H2 , , placed for donor A 11 ADE C2 . HBUILD: H8 , , placed for donor A 11 ADE C8 . HBUILD: H2' , , placed for donor A 11 ADE C2' . HBUILD: H3' , , placed for donor A 11 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 12 URI C5' . HBUILD: H4' , , placed for donor A 12 URI C4' . HBUILD: H1' , , placed for donor A 12 URI C1' . HBUILD: H6 , , placed for donor A 12 URI C6 . HBUILD: H3 , , placed for donor A 12 URI N3 . HBUILD: H5 , , placed for donor A 12 URI C5 . HBUILD: H2' , , placed for donor A 12 URI C2' . HBUILD: H3' , , placed for donor A 12 URI C3' . HBUILD: H5' ,H5'', placed for donor A 13 ADE C5' . HBUILD: H4' , , placed for donor A 13 ADE C4' . HBUILD: H1' , , placed for donor A 13 ADE C1' . HBUILD: H2 , , placed for donor A 13 ADE C2 . HBUILD: H8 , , placed for donor A 13 ADE C8 . HBUILD: H2' , , placed for donor A 13 ADE C2' . HBUILD: H3' , , placed for donor A 13 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 14 ADE C5' . HBUILD: H4' , , placed for donor A 14 ADE C4' . HBUILD: H1' , , placed for donor A 14 ADE C1' . HBUILD: H2 , , placed for donor A 14 ADE C2 . HBUILD: H8 , , placed for donor A 14 ADE C8 . HBUILD: H2' , , placed for donor A 14 ADE C2' . HBUILD: H3' , , placed for donor A 14 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 15 CYT C5' . HBUILD: H4' , , placed for donor A 15 CYT C4' . HBUILD: H1' , , placed for donor A 15 CYT C1' . HBUILD: H6 , , placed for donor A 15 CYT C6 . HBUILD: H5 , , placed for donor A 15 CYT C5 . HBUILD: H2' , , placed for donor A 15 CYT C2' . HBUILD: H3' , , placed for donor A 15 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 16 CYT C5' . HBUILD: H4' , , placed for donor A 16 CYT C4' . HBUILD: H1' , , placed for donor A 16 CYT C1' . HBUILD: H6 , , placed for donor A 16 CYT C6 . HBUILD: H5 , , placed for donor A 16 CYT C5 . HBUILD: H2' , , placed for donor A 16 CYT C2' . HBUILD: H3' , , placed for donor A 16 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 17 CYT C5' . HBUILD: H4' , , placed for donor A 17 CYT C4' . HBUILD: H1' , , placed for donor A 17 CYT C1' . HBUILD: H6 , , placed for donor A 17 CYT C6 . HBUILD: H5 , , placed for donor A 17 CYT C5 . HBUILD: H2' , , placed for donor A 17 CYT C2' . HBUILD: H3' , , placed for donor A 17 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 18 URI C5' . HBUILD: H4' , , placed for donor A 18 URI C4' . HBUILD: H1' , , placed for donor A 18 URI C1' . HBUILD: H6 , , placed for donor A 18 URI C6 . HBUILD: H3 , , placed for donor A 18 URI N3 . HBUILD: H5 , , placed for donor A 18 URI C5 . HBUILD: H2' , , placed for donor A 18 URI C2' . HBUILD: H3' , , placed for donor A 18 URI C3' . HBUILD: H5' ,H5'', placed for donor A 19 GUA C5' . HBUILD: H4' , , placed for donor A 19 GUA C4' . HBUILD: H1' , , placed for donor A 19 GUA C1' . HBUILD: H1 , , placed for donor A 19 GUA N1 . HBUILD: H8 , , placed for donor A 19 GUA C8 . HBUILD: H2' , , placed for donor A 19 GUA C2' . HBUILD: H3' , , placed for donor A 19 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 20 CYT C5' . HBUILD: H4' , , placed for donor A 20 CYT C4' . HBUILD: H1' , , placed for donor A 20 CYT C1' . HBUILD: H6 , , placed for donor A 20 CYT C6 . HBUILD: H5 , , placed for donor A 20 CYT C5 . HBUILD: H2' , , placed for donor A 20 CYT C2' . HBUILD: H3' , , placed for donor A 20 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 21 CYT C5' . HBUILD: H4' , , placed for donor A 21 CYT C4' . HBUILD: H1' , , placed for donor A 21 CYT C1' . HBUILD: H6 , , placed for donor A 21 CYT C6 . HBUILD: H5 , , placed for donor A 21 CYT C5 . HBUILD: H2' , , placed for donor A 21 CYT C2' . HBUILD: H3' , , placed for donor A 21 CYT C3' . HBUILD: H5T , , , constructed (spin) for donor A 1 GUA O5T . HBUILD: H21 ,H22 , , constructed (spin) for donor A 1 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 1 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 2 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 2 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 3 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 3 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 4 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 4 ADE O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 5 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 5 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 6 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 6 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 7 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 7 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 8 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 8 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 9 URI O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 10 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 10 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 11 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 11 ADE O2' . HBUILD: HO2', , , constructed (spin) for donor A 12 URI O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 13 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 13 ADE O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 14 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 14 ADE O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 15 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 15 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 16 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 16 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 17 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 17 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 18 URI O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 19 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 19 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 20 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 20 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 21 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 21 CYT O2' . HBUILD: H3T , , , constructed (spin) for donor A 21 CYT O3' . X-PLOR> X-PLOR>flags include vdw end X-PLOR>minimize powell nstep=800 nprint=50 end POWELL: number of degrees of freedom= 2031 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 9611 intra-atom interactions NBONDS: found 9605 intra-atom interactions NBONDS: found 9629 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =415.615 grad(E)=20.923 E(BOND)=34.386 E(ANGL)=152.201 | | E(DIHE)=0.000 E(IMPR)=170.039 E(VDW )=58.990 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =199.585 grad(E)=3.266 E(BOND)=10.886 E(ANGL)=116.803 | | E(DIHE)=0.000 E(IMPR)=18.333 E(VDW )=53.563 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =182.939 grad(E)=2.642 E(BOND)=9.987 E(ANGL)=112.133 | | E(DIHE)=0.000 E(IMPR)=12.408 E(VDW )=48.411 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =176.743 grad(E)=1.666 E(BOND)=9.537 E(ANGL)=108.616 | | E(DIHE)=0.000 E(IMPR)=12.622 E(VDW )=45.968 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =170.795 grad(E)=1.746 E(BOND)=9.278 E(ANGL)=105.255 | | E(DIHE)=0.000 E(IMPR)=13.112 E(VDW )=43.151 | ------------------------------------------------------------------------------- NBONDS: found 9649 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =161.558 grad(E)=2.474 E(BOND)=8.802 E(ANGL)=100.502 | | E(DIHE)=0.000 E(IMPR)=13.512 E(VDW )=38.741 | ------------------------------------------------------------------------------- --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =151.225 grad(E)=2.485 E(BOND)=7.993 E(ANGL)=93.958 | | E(DIHE)=0.000 E(IMPR)=13.403 E(VDW )=35.871 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =140.322 grad(E)=2.307 E(BOND)=7.516 E(ANGL)=90.333 | | E(DIHE)=0.000 E(IMPR)=12.294 E(VDW )=30.181 | ------------------------------------------------------------------------------- --------------- cycle= 450 ------ stepsize= 0.0000 ----------------------- | Etotal =130.273 grad(E)=1.902 E(BOND)=7.001 E(ANGL)=86.112 | | E(DIHE)=0.000 E(IMPR)=11.646 E(VDW )=25.514 | ------------------------------------------------------------------------------- NBONDS: found 9691 intra-atom interactions --------------- cycle= 500 ------ stepsize= 0.0000 ----------------------- | Etotal =122.710 grad(E)=1.619 E(BOND)=6.421 E(ANGL)=81.717 | | E(DIHE)=0.000 E(IMPR)=11.426 E(VDW )=23.146 | ------------------------------------------------------------------------------- --------------- cycle= 550 ------ stepsize= 0.0000 ----------------------- | Etotal =118.152 grad(E)=1.530 E(BOND)=6.218 E(ANGL)=79.123 | | E(DIHE)=0.000 E(IMPR)=10.745 E(VDW )=22.066 | ------------------------------------------------------------------------------- --------------- cycle= 600 ------ stepsize= 0.0000 ----------------------- | Etotal =114.473 grad(E)=1.400 E(BOND)=5.951 E(ANGL)=76.474 | | E(DIHE)=0.000 E(IMPR)=10.455 E(VDW )=21.593 | ------------------------------------------------------------------------------- NBONDS: found 9738 intra-atom interactions --------------- cycle= 650 ------ stepsize= 0.0000 ----------------------- | Etotal =110.349 grad(E)=1.666 E(BOND)=5.256 E(ANGL)=73.736 | | E(DIHE)=0.000 E(IMPR)=10.634 E(VDW )=20.723 | ------------------------------------------------------------------------------- --------------- cycle= 700 ------ stepsize= 0.0000 ----------------------- | Etotal =106.278 grad(E)=1.348 E(BOND)=5.047 E(ANGL)=71.561 | | E(DIHE)=0.000 E(IMPR)=10.148 E(VDW )=19.521 | ------------------------------------------------------------------------------- --------------- cycle= 750 ------ stepsize= 0.0000 ----------------------- | Etotal =101.587 grad(E)=1.314 E(BOND)=4.678 E(ANGL)=70.390 | | E(DIHE)=0.000 E(IMPR)=9.901 E(VDW )=16.618 | ------------------------------------------------------------------------------- --------------- cycle= 800 ------ stepsize= 0.0000 ----------------------- | Etotal =98.289 grad(E)=1.181 E(BOND)=4.156 E(ANGL)=69.121 | | E(DIHE)=0.000 E(IMPR)=9.602 E(VDW )=15.411 | ------------------------------------------------------------------------------- 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>! Total energy should be no more than about 100. If it is, it is probably X-PLOR>! because one or more purines are trapped in a crumpled conformation. X-PLOR> X-PLOR>flags exclude * include bond angle dihe impr vdw end X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.002 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.153589E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.589 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.588708 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 0.000000E+00 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.271 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.270697 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 4.15562, angle 69.1207, dihedral 0, improper 9.60187, VdW 15.4106, total 98.2888 RMSD: bond 1.535891E-03, angle 0.588708, dihedral 0, improper 0.270697 Violations: bond 0, angle 0, dihedral 0, improper 0 X-PLOR> X-PLOR>write coordinates output=template.pdb end ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/template.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 98626 current use= 0 X-PLOR: total CPU time= 42.0275 s X-PLOR: entry time at 13:39:07 27-Apr-96 X-PLOR: exit time at 13:39:50 27-Apr-96