table of contents
g_dyndom(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_dyndom(1) |
NAME¶
g_dyndom - interpolate and extrapolate structure rotationsSYNOPSIS¶
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 vectorDESCRIPTION¶
g_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 g_confrms) rather than by file comparison (using diff).FILES¶
-f dyndom.pdb InputProtein data bank file
Trajectory: xtc trr trj gro g96 pdb
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
Angle of rotation about rotation vector
Angle of rotation about rotation vector
Number of steps on the pathway
DymDom dtermined angle of rotation about rotation vector
Translation (Angstrom) along rotation vector (see DynDom info file)
First atom of the arrow vector
Last atom of the arrow vector
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |