NAME

       g_dyndom - interpolate and extrapolate structure rotations

       VERSION 4.6.5

SYNOPSIS

       g_dyndom  -f  dyndom.pdb  -o  rotated.xtc  -n  domains.ndx  -[no]h  -[no]version -nice int
       -firstangle real -lastangle real -nframe int -maxangle real -trans real -head vector -tail
       vector

DESCRIPTION

         g_dyndom  reads  a  .pdb file output from DynDom (http://www.cmp.uea.ac.uk/dyndom/).  It
       reads the coordinates, the coordinates of the rotation axis, and an index file  containing
       the  domains.   Furthermore, it takes the first and last atom of the arrow file as command
       line arguments (head and tail) and finally it  takes  the  translation  vector  (given  in
       DynDom info file) and the angle of rotation (also as command line arguments). If the angle
       determined by DynDom is given, one should be able to recover the second structure used for
       generating  the  DynDom  output.   Because  of  limited  numerical accuracy this should be
       verified by computing an all-atom RMSD (using  g_confrms) rather than by  file  comparison
       (using diff).

       The  purpose  of  this  program is to interpolate and extrapolate the rotation as found by
       DynDom. As a result unphysical structures with long or short bonds, or  overlapping  atoms
       may  be  produced. Visual inspection, and energy minimization may be necessary to validate
       the structure.

FILES

       -f dyndom.pdb Input
        Protein data bank file

       -o rotated.xtc Output
        Trajectory: xtc trr trj gro g96 pdb

       -n domains.ndx Input
        Index file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        Set the nicelevel

       -firstangle real 0
        Angle of rotation about rotation vector

       -lastangle real 0
        Angle of rotation about rotation vector

       -nframe int 11
        Number of steps on the pathway

       -maxangle real 0
        DymDom dtermined angle of rotation about rotation vector

       -trans real 0
        Translation (Angstrom) along rotation vector (see DynDom info file)

       -head vector 0 0 0
        First atom of the arrow vector

       -tail vector 0 0 0
        Last atom of the arrow vector

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                          Mon 2 Dec 2013                              g_dyndom(1)