1genrestr(1)               GROMACS suite, VERSION 4.5               genrestr(1)
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NAME

6       genrestr  -  generates  position  restraints or distance restraints for
7       index groups
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9       VERSION 4.5
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SYNOPSIS

12       genrestr -f conf.gro -n index.ndx -o posre.itp  -of  freeze.ndx  -[no]h
13       -[no]version  -nice  int -fc vector -freeze real -[no]disre -disre_dist
14       real -disre_frac real -disre_up2 real -cutoff real -[no]constr
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DESCRIPTION

17       genrestr produces an include file for a topology containing a  list  of
18       atom  numbers and three force constants for the X, Y and Z direction. A
19       single isotropic force constant  may  be  given  on  the  command  line
20       instead of three components.
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23       WARNING:  position restraints only work for the one molecule at a time.
24       Position restraints are interactions within molecules,  therefore  they
25       should  be  included  within the correct  [ moleculetype ] block in the
26       topology. Since the atom numbers in every moleculetype in the  topology
27       start  at 1 and the numbers in the input file for genpr number consecu‐
28       tively from 1, genpr will only produce a useful file for the first mol‐
29       ecule.
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32       The  -of  option  produces  an index file that can be used for freezing
33       atoms. In this case the input file must be a pdb file.
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36       With the  -disre option half a matrix of distance restraints is  gener‐
37       ated  instead  of position restraints. With this matrix, that one typi‐
38       cally would apply to C-alpha atoms in a protein, one can  maintain  the
39       overall conformation of a protein without tieing it to a specific posi‐
40       tion (as with position restraints).
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FILES

43       -f conf.gro Input
44        Structure file: gro g96 pdb tpr etc.
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46       -n index.ndx Input, Opt.
47        Index file
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49       -o posre.itp Output
50        Include file for topology
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52       -of freeze.ndx Output, Opt.
53        Index file
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OTHER OPTIONS

57       -[no]hno
58        Print help info and quit
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60       -[no]versionno
61        Print version info and quit
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63       -nice int 0
64        Set the nicelevel
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66       -fc vector 1000 1000 1000
67        force constants (kJ mol-1 nm-2)
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69       -freeze real 0
70        if the -of option or this one is given an index file will  be  written
71       containing atom numbers of all atoms that have a B-factor less than the
72       level given here
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74       -[no]disreno
75        Generate a distance restraint matrix for all the atoms in index
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77       -disre_dist real 0.1
78        Distance range around the  actual  distance  for  generating  distance
79       restraints
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81       -disre_frac real 0
82        Fraction  of  distance to be used as interval rather than a fixed dis‐
83       tance. If the fraction of the distance that you specify  here  is  less
84       than  the  distance  given  in  the  previous  option, that one is used
85       instead.
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87       -disre_up2 real 1
88        Distance between upper bound for distance restraints, and the distance
89       at which the force becomes constant (see manual)
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91       -cutoff real -1
92        Only generate distance restraints for atoms pairs within cutoff (nm)
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94       -[no]constrno
95        Generate  a  constraint  matrix  rather than distance restraints. Con‐
96       straints of type 2 will be generated that do generate exclusions.
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SEE ALSO

100       gromacs(7)
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102       More  information  about  GROMACS  is  available  at   <http://www.gro‐
103       macs.org/>.
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107                                Thu 26 Aug 2010                    genrestr(1)
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