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)