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et_paths options trajectory_file


Mode - pathway analysis or packing density

Options for both pathway and packing density calculations

Options for pathway analysis only

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
  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
  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
  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
  atoms: "25"

# Pathways containing some of selected atoms 
  atoms: "102-110" # A list of atoms in cuby selection syntax


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.