man genpr (Commandes) - genpr VERSION 3.3_beta_20050823
NAME
genpr VERSION 3.3_beta_20050823
SYNOPSIS
genpr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -nice int -fc vector -freeze real
DESCRIPTION
genpr produces an include file for a topology containing a list of atom numbers and three force constants for the X, Y and Z direction. A single isotropic force constant may be given on the command line instead of three components.
WARNING: genpr only works for the first molecule. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ]
block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genpr number consecutively from 1, genpr will only produce a useful file for the first molecule.
The -of option produces an index file that can be used for freezing atoms. In this case the input file must be a pdb file.
FILES
-f conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml
-n index.ndx Input, Opt. Index file
-o posre.itp Output Include file for topology
-of freeze.ndx Output, Opt. Index file
OTHER OPTIONS
-[no]h no Print help info and quit
-nice int 0 Set the nicelevel
-fc vector 1000 1000 1000 force constants (kJ mol-1 nm-2)
-freeze real 0 if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here