table of contents
g_helixorient(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_helixorient(1) |
NAME¶
g_helixorient - calculates local pitch/bending/rotation/orientation inside helicesSYNOPSIS¶
g_helixorient -s topol.tpr -f traj.xtc -n index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise rise.xvg -oradius radius.xvg -otwist twist.xvg -obending bending.xvg -otilt tilt.xvg -orot rotation.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -[no]sidechain -[no]incrementalDESCRIPTION¶
g_helixorient calculates the coordinates and direction of the average axis inside an alpha helix, and the direction/vectors of both the Calpha and (optionally) a sidechain atom relative to the axis.FILES¶
-s topol.tpr InputRun input file: tpr tpb tpa
Trajectory: xtc trr trj gro g96 pdb cpt
Index file
Generic data file
Generic data file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
xvg plot formatting: xmgrace, xmgr or none
Calculate sidechain directions relative to helix axis too.
Calculate incremental rather than total rotation/tilt.
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |