genrestr

Main Table of Contents

VERSION 4.6.4
Wed 13 Nov 2013

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 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

optionfilenametypedescription
-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

optiontypedefaultdescription
-[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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