gmx-genrestr man page
gmx-genrestr — Generate position restraints or distance restraints for index groups
gmx genrestr [-f [<.gro/.g96/...>]
] [-n [<.ndx>]
] [-o [<.itp>]
] [-of [<.ndx>]
] [-fc <vector>
] [-freeze <real>
] [-disre_dist <real>
] [-disre_frac <real>
] [-disre_up2 <real>
] [-cutoff <real>
gmx 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 based on the contents of the -f file. A single isotropic force constant may be given on the command line instead of three components.
WARNING: Position restraints are interactions within molecules, therefore they must be included within the correct [ moleculetype ] block in the topology. The atom indices within the [ position_restraints ] block must be within the range of the atom indices for that molecule type. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for gmx genrestr number consecutively from 1, gmx genrestr will only produce a useful file for the first molecule. You may wish to edit the resulting index file to remove the lines for later atoms, or construct a suitable index group to provide as input to gmx genrestr.
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).
Options to specify input files:
- -f [<.gro/.g96/…>] (conf.gro)
Structure file: gro g96 pdb brk ent esp tpr
- -n [<.ndx>] (index.ndx) (Optional)
Options to specify output files:
- -o [<.itp>] (posre.itp)
Include file for topology
- -of [<.ndx>] (freeze.ndx) (Optional)
- -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 (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 (no)
Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.
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