genpr(1)
NAME
genpr - generates position restraints for index groups
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
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.