1GMX-DYNDOM(1)                       GROMACS                      GMX-DYNDOM(1)
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NAME

6       gmx-dyndom - Interpolate and extrapolate structure rotations
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SYNOPSIS

9          gmx dyndom [-f [<.pdb>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
10                     [-firstangle <real>] [-lastangle <real>] [-nframe <int>]
11                     [-maxangle <real>] [-trans <real>] [-head <vector>]
12                     [-tail <vector>]
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DESCRIPTION

15       gmx    dyndom    reads    a   .pdb   file   output   from   DynDom   (‐
16       http://www.cmp.uea.ac.uk/dyndom/).  It reads the coordinates, the coor‐
17       dinates of the rotation axis, and an index file containing the domains.
18       Furthermore, it takes the first and last atom of the arrow file as com‐
19       mand  line  arguments (head and tail) and finally it takes the transla‐
20       tion vector (given in DynDom info file) and the angle of rotation (also
21       as command line arguments). If the angle determined by DynDom is given,
22       one should be able to recover the second structure used for  generating
23       the  DynDom  output.  Because of limited numerical accuracy this should
24       be verified by computing an all-atom RMSD (using  gmx  confrms)  rather
25       than by file comparison (using diff).
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27       The purpose of this program is to interpolate and extrapolate the rota‐
28       tion as found by DynDom. As a result unphysical structures with long or
29       short  bonds,  or overlapping atoms may be produced. Visual inspection,
30       and energy minimization may be necessary to validate the structure.
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OPTIONS

33       Options to specify input files:
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35       -f [<.pdb>] (dyndom.pdb)
36              Protein data bank file
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38       -n [<.ndx>] (domains.ndx)
39              Index file
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41       Options to specify output files:
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43       -o [<.xtc/.trr/…>] (rotated.xtc)
44              Trajectory: xtc trr gro g96 pdb tng
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46       Other options:
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48       -firstangle <real> (0)
49              Angle of rotation about rotation vector
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51       -lastangle <real> (0)
52              Angle of rotation about rotation vector
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54       -nframe <int> (11)
55              Number of steps on the pathway
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57       -maxangle <real> (0)
58              DymDom dtermined angle of rotation about rotation vector
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60       -trans <real> (0)
61              Translation (Angstrom) along rotation vector  (see  DynDom  info
62              file)
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64       -head <vector> (0 0 0)
65              First atom of the arrow vector
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67       -tail <vector> (0 0 0)
68              Last atom of the arrow vector
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SEE ALSO

71       gmx(1)
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73       More     information    about    GROMACS    is    available    at    <‐
74       http://www.gromacs.org/>.
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77       2019, GROMACS development team
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822019.2                           Apr 16, 2019                    GMX-DYNDOM(1)
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