genrestr - generates position restraints or distance restraints for
genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h
-nice int -fc vector -freeze real -[no]disre -disre_dist real
-disre_frac real -disre_up2 real -[no]constr
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 genpr number
consecutively from 1, genpr will only produce a useful file for the
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 C-alpha 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 tpb tpa
-n index.ndx Input, Opt.
-o posre.itp Output
Include file for topology
-of freeze.ndx Output, Opt.
Print help info and quit
-nice int 0
Set the nicelevel
-fc vector 1000 1000 1000
force constants (kJ mol-1 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
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
-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
-disre_up2 real 1
Distance between upper bound for distance restraints, and the distance
at which the force becomes constant (see manual)
Generate a constraint matrix rather than distance restraints
More information about GROMACS is available at
Thu 16 Oct 2008 genrestr(1)