genpr1
Generates position restraints for index groups
Usage
genpr -f
conf.gro
-n
index.ndx
-o
posre.itp
-of
freeze.ndx
-
[no]
h
-nice
int
-fc
vector
-freeze
real
Overview
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
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
Releases
2 releases since Debian 4.0 (Etch); the text changed 1 time.