et_paths
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) 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: 1.4Tube 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.