NAME

       genrestr - generates position restraints or distance restraints for index groups

       VERSION 4.6.5

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 typically 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 2 Dec 2013                              genrestr(1)