g_bundle(1)
NAME
g_bundle - analyzes bundles of axes, e.g. transmembrane helices
SYNOPSIS
g_bundle -f traj.xtc -s topol.tpr -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]xvgr -na int -[no]z
DESCRIPTION
g_bundle analyzes bundles of axes. The axes can be for instance helix
axes. The program reads two index groups and divides both of them in
-na parts. The centers of mass of these parts define the tops and bottoms of the axes. Several quantities are written to file: the axis
length, the distance and the z-shift of the axis mid-points with
respect to the average center of all axes, the total tilt, the radial
tilt and the lateral tilt with respect to the average axis.
With options -ok , -okr and -okl the total, radial and lateral kinks of
the axes are plotted. An extra index group of kink atoms is required,
which is also divided into -na
parts. The kink angle is defined as the angle between the kink-top and
the bottom-kink vectors.
With option -oa the top, mid (or kink when -ok is set) and bottom
points of each axis are written to a pdb file each frame. The residue
numbers correspond to the axis numbers. When viewing this file with
rasmol , use the command line option -nmrpdb , and type set axis true
to display the reference axis.
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index file
- -ol bun_len.xvg Output
- xvgr/xmgr file
- -od bun_dist.xvg Output
- xvgr/xmgr file
- -oz bun_z.xvg Output
- xvgr/xmgr file
- -ot bun_tilt.xvg Output
- xvgr/xmgr file
- -otr bun_tiltr.xvg Output
- xvgr/xmgr file
- -otl bun_tiltl.xvg Output
- xvgr/xmgr file
- -ok bun_kink.xvg Output, Opt.
- xvgr/xmgr file
- -okr bun_kinkr.xvg Output, Opt.
- xvgr/xmgr file
- -okl bun_kinkl.xvg Output, Opt.
- xvgr/xmgr file
- -oa axes.pdb Output, Opt.
- Protein data bank file
OTHER OPTIONS
- -[no]h no
- 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)
- -tu enum ps
- Time unit: ps , fs , ns , us , ms , s , m or h
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -na int 0
- Number of axes
- -[no]z no
- Use the Z-axis as reference iso the average axis
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.