NAME
g_helixorient - calculates local pitch/bending/rotation/orientation
inside helices
VERSION 4.0.1
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 -nice int -b time -e time -dt time -[no]xvgr
-[no]sidechain -[no]incremental
DESCRIPTION
g_helixorient calculates coordinates and direction of the average axis
inside an alpha helix, and the direction/vectors of both the alpha
carbon and (optionally) a sidechain atom relative to the axis.
As input, you need to specify an index group with alpha carbon 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/CA-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 theta1-3.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
-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)
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[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/>.
Thu 16 Oct 2008 g_helixorient(1)