gmx-dyndom(1) GROMACS Manual gmx-dyndom(1)NAMEgmx-dyndom - Interpolate and extrapolate structure rotations
SYNOPSIS
gmx dyndom [-f [<.pdb>]] [-o [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-nice <int>] [-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 coor‐
dinates of the rotation axis, and an index file containing the domains.
Furthermore, it takes the first and last atom of the arrow file as com‐
mand line arguments (head and tail) and finally it takes the transla‐
tion 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 rota‐
tion 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 and output files:
-f [<.pdb>] (dyndom.pdb) (Input)
Protein data bank file
-o [<.xtc/.trr/...>] (rotated.xtc) (Output)
Trajectory: xtc trr trj gro g96 pdb tng
-n [<.ndx>] (domains.ndx) (Input)
Index file
Other options:
-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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-dyndom(1)