genrestr produces an include file for a topology containing
a list of atom numbers and three force constants for the
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).
|-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|
|-[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.|