man g_bundle (Commandes) - g_bundle VERSION 3.3_beta_20050823
NAME
g_bundle VERSION 3.3_beta_20050823
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