! dg.inp -- Full metric matrix distance geometry
! Dave Schweisguth <dcs@proton.chem.yale.edu>, 7 May 1996
! Derived from nmr/dg_full_embed.inp

set seed=@xplor.seed end	    ! Use 'xplor -s'

set echo=off message=off end	    ! Normal use
!set echo=on message=all end	    ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end
! Uncomment the following to define rigid groups (which seem to do nothing)
!coordinates disposition=main @template.pdb	    ! END in PDB file

noe nres=1000 @noes.stem.inp @noes.loop.inp @base-pairs.inp end
restraints dihedral nassign=300 @dihedrals.inp end

set echo=on message=all end

! Include NOE and dihedral restraints in mmdg

flags exclude * include bond angle dihe impr vdw noe cdih end
parameter nbonds repel=0.8 end end  ! Scale van der Waals radii

mmdg
!    @groups.inp		    ! Uncomment to define rigid groups
				    ! (which seem to do nothing)
    selection=(all)
    storebounds
end

! Loop until embedding is successful. Once usually suffices.

evaluate ($embedded="false")
while ($embedded="false") loop embed
    mmdg recallbounds end
end loop embed

! Scale coordinates by $dgscale (defined by mmdg)

vector do (x = x * $dgscale) (known)
vector do (y = y * $dgscale) (known)
vector do (z = z * $dgscale) (known)

! Regularize

flags exclude * include dg end
minimize powell nstep=100 drop=10 nprint=25 end

write coordinates output=dg.pdb end
   
stop