NAME
g_dyndom - interpolate and extrapolate structure rotations
VERSION 4.0.1
SYNOPSIS
g_dyndom -f dyndom.pdb -o rotated.xtc -n domains.ndx -[no]h -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, and the
coordinates of the rotation axis furthermore it reads 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
-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 (Aangstroem) 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/>.
Thu 16 Oct 2008 g_dyndom(1)