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       genrestr  -  generates  position  restraints or distance restraints for
       index groups

       VERSION 4.0.1


       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
       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).


       -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


        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)