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genpr

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.