genrestr(1)

NAME

genrestr - generates position restraints or distance restraints for index groups

VERSION 4.0.1

SYNOPSIS

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

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 genpr number consecutively from 1, genpr 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 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).

FILES

-f conf.gro Input

Structure file: gro g96 pdb tpr tpb tpa

-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

-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

-[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 dis

tance. 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)

-[no]constrno

Generate a constraint matrix rather than distance restraints

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

Thu 16 Oct 2008 genrestr(1)