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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) used when trajectory format contains only coordinates but not element specifiaction * '''-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. Parameterd for X...pi interactions are used instead of vacuum ones for these atoms. * '''-x, -^-exclude''' Selection of atoms excluded from calculation * '''-c, -^-conductive''' Bonds between atoms in provided lists are conductive (decay factor 1) * '''-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''' Do not use ring bridges for selected atoms * '''-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}} !! Tube definition The "tubes" (pathway types) can be assigned automatically based on a tube definitions provided in a file. Following example explains possible conditions used. A pathway must satisfy all these conditions to belong to a given tube. Multiple selections, separated by ";", can be provided. The condition must be satisfied for each selection separately. {{# Pathways with 2 hydrogen bonds, atoms 21 and 232 are involved hydrogen bond A1: atoms: "21" # A path must contain atom in the selection hb_count: 2 # Number or range of hydrogen bonds hb_at: 21;232 # An atom in the selection must be involved in hydrogen bond. # Pathways with 3 hydrogen bonds, atoms 21 and 232 are involved hydrogen bond A2: atoms: "21" hb_count: 3 hb_at: 21;232 # Pathways with 1..3 vacuum jumps and no more than 1 H-bond # contains both atom 21 and 232 A3: atoms: "21;232" hb_count: 0..1 vac_count: 1..3 # vac_count and vac_at are anaogous to hb_..., but for vacuum jumps # Pathways containing atom 25 B: atoms: "25" # Pathways containing some of selected atoms D: atoms: "102-110" # A list of atoms in cuby selection syntax }} !Visualization 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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