xenial (1) gmx-dyndom.1.gz

NAME

       gmx-dyndom - Interpolate and extrapolate structure rotations

SYNOPSIS

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

DESCRIPTION

       gmx  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 gmx 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.

OPTIONS

       Options to specify input files:

       -f [<.pdb>] (dyndom.pdb)
              Protein data bank file

       -n [<.ndx>] (domains.ndx)
              Index file

       Options to specify output files:

       -o [<.xtc/.trr/...>] (rotated.xtc)
              Trajectory: xtc trr gro g96 pdb tng

       Other options:

       -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

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team