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g_bundleMain Table of Contents |
VERSION 4.6.4
Wed 13 Nov 2013
| VERSION 4.6.4 |
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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[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 |