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)
