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genprMain Table of Contents |
VERSION 4.6
Sat 19 Jan 2013
| VERSION 4.6 |
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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | 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 |