genrestr(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c genrestr(1)
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 typi-
cally 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)
-[no]constrno
Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 genrestr(1)