debian man page for g_dyndom

g_dyndom(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_dyndom(1)

NAME
       g_dyndom - interpolate and extrapolate structure rotations

       VERSION 4.5.4-dev-20110404-bc5695c

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 rota-
       tion axis, and an index file containing the domains.  Furthermore, it takes the first and last atom of the arrow file as command line argu-
       ments (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  struc-
       ture.

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 4 Apr 2011						       g_dyndom(1)