g_helixorient(1)
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
- More information about GROMACS is available at <http://www.gromacs.org/>.