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{BACK:Tools} !Method !Usage {html}<pre>et_paths options trajectory_file</pre>{/html} !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: {{# Hydrogen bond hb_rterm_k: -0.6418 # radial hb_rterm_r: 2.01313 # radial hb_aterm_k: -2.2345 # angular hb_mixed_k: -1.8346 # radial + angular hb_mixed_r: 2.01313 # radial + angular # X...pi interaction pi_k: -1.7 pi_r: 2.2 # Plain vacuum vac_k: -1.7 vac_r: 1.4}} The 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. !References
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