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et_paths

This revision is from 2010/11/30 15:04. 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:

# 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.

A1:
  atoms: "21" # A path must contain atom in the selection
  hb_count: 2 # Number or range of hydrogen bonds
  hb_at: 21;232 # Hydrogen bond contain atom in the selection. Multiple selections are separated by ;, condition must be satisfied for each group of atoms

A2:
  atoms: "21"
  hb_count: 3
  hb_at: 21;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

B:
  atoms: "25"

C:
  atoms: "47"

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