g_helixorient (1) Linux Manual Page

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/>.