genpr

| ## genpr Main Table of Contents | VERSION 4.0 Sun 18 Jan 2009

### 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

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

### Other options

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

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