NAME

       g_helixorient - calculates local pitch/bending/rotation/orientation inside helices

       VERSION 4.6.5

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 2 Dec 2013                         g_helixorient(1)