## genrestr

Main Table of Contents

VERSION 4.6
Sat 19 Jan 2013

### Description

`genrestr` produces an include file for a topology containing a list of atom numbers and three force constants for the <it>x</it>-, <it>y</it>-, and <it>z</it>-direction. A single isotropic force constant may be given on the command line instead of three components.

WARNING: position restraints only work for the one molecule at a time. 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 `genrestr` number consecutively from 1, `genrestr` 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.

With the `-disre` option, half a matrix of distance restraints is generated instead of position restraints. With this matrix, that one typically would apply to Cα atoms in a protein, one can maintain the overall conformation of a protein without tieing it to a specific position (as with position restraints).

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `conf.gro` | Input | Structure file: gro g96 pdb tpr etc.
`-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
`-[no]version` | bool | `no` | Print version info and quit
`-nice` | int | `0` | Set the nicelevel
`-fc` | vector | `1000 1000 1000` | Force constants (kJ/mol 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
`-[no]disre` | bool | `no` | Generate a distance restraint matrix for all the atoms in index
`-disre_dist` | real | `0.1` | Distance range around the actual distance for generating distance restraints
`-disre_frac` | real | `0` | Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead.
`-disre_up2` | real | `1` | Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)
`-cutoff` | real | `-1` | Only generate distance restraints for atoms pairs within cutoff (nm)
`-[no]constr` | bool | `no` | Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.

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