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 helices
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
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]incremental
DESCRIPTION
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.
As input, you need to specify an index group with Calpha atoms corresponding to an alpha-helix of continuous residues. Sidechain directions
require a second index group of the same size, containing the heavy atom in each residue that should represent the sidechain.
Note that this program does not do any fitting of structures.
We need four Calpha coordinates to define the local direction of the helix axis.
The tilt/rotation is calculated from Euler rotations, where we define the helix axis as the local x-axis, the residues/Calpha vector as
y, and the z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we first tilt the helix axis (1) around and (2)
orthogonal to the residues vector, and finally apply the (3) rotation around it. For debugging or other purposes, we also write out the
actual Euler rotation angles as theta[1-3].xvg
FILES
-s topol.tpr Input
Run input file: tpr tpb tpa
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input, Opt.
Index file
-oaxis helixaxis.dat Output
Generic data file
-ocenter center.dat Output
Generic data file
-orise rise.xvg Output
xvgr/xmgr file
-oradius radius.xvg Output
xvgr/xmgr file
-otwist twist.xvg Output
xvgr/xmgr file
-obending bending.xvg Output
xvgr/xmgr file
-otilt tilt.xvg Output
xvgr/xmgr file
-orot rotation.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]sidechainno
Calculate sidechain directions relative to helix axis too.
-[no]incrementalno
Calculate incremental rather than total rotation/tilt.
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_helixorient(1)