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)