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

6       g_dyndom - interpolate and extrapolate structure rotations
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8       VERSION 4.5
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SYNOPSIS

11       g_dyndom  -f  dyndom.pdb -o rotated.xtc -n domains.ndx -[no]h -[no]ver‐
12       sion -nice int -firstangle real -lastangle real -nframe  int  -maxangle
13       real -trans real -head vector -tail vector
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DESCRIPTION

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

35       -f dyndom.pdb Input
36        Protein data bank file
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38       -o rotated.xtc Output
39        Trajectory: xtc trr trj gro g96 pdb
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41       -n domains.ndx Input
42        Index file
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OTHER OPTIONS

46       -[no]hno
47        Print help info and quit
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49       -[no]versionno
50        Print version info and quit
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52       -nice int 0
53        Set the nicelevel
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55       -firstangle real 0
56        Angle of rotation about rotation vector
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58       -lastangle real 0
59        Angle of rotation about rotation vector
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61       -nframe int 11
62        Number of steps on the pathway
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64       -maxangle real 0
65        DymDom dtermined angle of rotation about rotation vector
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67       -trans real 0
68        Translation (Aangstroem) along rotation vector (see DynDom info file)
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70       -head vector 0 0 0
71        First atom of the arrow vector
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73       -tail vector 0 0 0
74        Last atom of the arrow vector
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SEE ALSO

78       gromacs(7)
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80       More  information  about  GROMACS  is  available  at   <http://www.gro‐
81       macs.org/>.
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85                                Thu 26 Aug 2010                    g_dyndom(1)
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