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g_bundle_d

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.