g_genrestr(1) - Linux man page

Name

genrestr - generates position restraints or distance restraints for

index groups

VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -[no]version -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -cutoff real -[no]constr

Description

genrestr 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: 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 Calpha 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

-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

-[no]hno Print help info and quit

-[no]versionno Print version info and quit

-nice int 0 Set the nicelevel

-fc vector 1000 1000 1000 force constants (kJ/mol nm2)

-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]disreno 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)