Remarks cad_xplor_minim_inp.txt
Remarks Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 04:32:07 2008 for A. Nonymous
Remarks Auto-generated by XPLO2D from file cad_exp.pdb
Remarks Energy-minimisation input file for residue type CAD

topology
!  @tophcsdx.pro
  @cad_xplor_top.txt
end

parameters
!  @parhcsdx.pro
  @cad_xplor_par.txt
  nbonds
    atom cdie shift eps=8.0  e14fac=0.4
    cutnb=7.5 ctonnb=6.0 ctofnb=6.5
    nbxmod=5 vswitch
  end
  remark dielectric constant eps set to 8.0
end

flags exclude elec ? end

segment name="    "
  chain
   coordinates @cad_clean.pdb
  end
end
coordinates @cad_clean.pdb

! Remarks Build hydrogens (if any)
! hbuild
!   selection = (hydrogen and not known)
!   phistep=45
! end

Remarks DELETE hydrogens and unknown atoms
delete
  selection = (hydrogen or (not known))
end

! Remarks If you want to shake up the coordinates a bit ...
! do (x=x+rand(0.1)-0.05) (all)
! do (y=y+rand(0.1)-0.05) (all)
! do (z=z+rand(0.1)-0.05) (all)

print threshold=0.02 bonds
print threshold=3.0 angles
print threshold=3.0 dihedrals
print threshold=3.0 impropers

Remarks Do Powell energy minimisation
minimise powell
  nstep=250 drop=40.0
end

write coordinates output=cad_min.pdb end
write structure   output=cad.psf end

! constraints interaction (not hydro) (not hydro) end

print threshold=0.02 bonds
print threshold=3.0 angles
print threshold=3.0 dihedrals
print threshold=3.0 impropers

flags exclude * include vdw end energy end
distance from=(not hydro) to=(not hydro) cutoff=2.6 end

stop