Main Table of Contents

Fri 5 Jul 2013


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.


-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-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 bool no Print help info and quit
-[no]version bool no 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)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-na int 0 Number of axes
-[no]z bool no Use the z-axis as reference instead of the average axis