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et_paths
This revision is from 2010/11/30 14:55. You can Restore it.
Method
Usage
et_paths options trajectory_file
Options
Mode - pathway analysis or packing density
- -d, --density Use desity packing model instead of pathway anaysis
Options for both pathway and packing density calculations
- -s, --start Index of start atom (numbering starts at 1)
- -e, --end Index of end atom (numbering starts at 1)
- -g, --reference_geometry Reference geometry (xyz or pdb file)
- -f, --format Trajectory format: xyz, pdb, amber, amber_box, xyz_notitle_noelement (default xyz)
- -S, --stride Analyze only every Nth frame (default 1)
Options for pathway analysis only
- -o, --output_file File containing path geometries (default is paths.pdb)
- -w, --write-traj Write trajectory of analyzed frames in .xyz format
- -p, --pi_atoms Selection of atoms having pi orbitals
- -x, --exclude Selection of atoms excluded from calculation
- -c, --conductive Bonds between atoms in provided lists are conductive
- -b, --beratan Original parameters by Beratan
- -P, --parameters File with custom parameters
- -k, --k-best-paths Number of paths reported
- -K, --discard-equivalent-paths List only paths that differ by coupling
- -r, --ring-bridges Avoid multiple equivalent pathways by bridging rings
- -R, --exclude-ring-bridges Exclude selected rings from ring bridges
- -t, --tubes File with tube definitions
- -h, --help Print help and exit
Files used
Parameters of pathway model
Here is commented sample of parameter file containing the default parameters:
hb_rterm_k: -0.6418
hb_rterm_r: 2.01313
hb_aterm_k: -2.2345
hb_mixed_k: -1.8346
hb_mixed_r: 2.01313
pi_k: -1.7
pi_r: 2.2
vac_k: -1.7
vac_r: 1.4The output geometry file (paths.pdb by default) contains the path(s) in format that can be visualized. The first frame is added to establish the connectivity in this path (when using VMD), and it should be removed after the trajectory is loaded.