Folder specifications:
EDHB: binary file for linux. This file cannot be edited. Standalone for EDHB. Do not require python.
scripts: Original python script.
examples: The examples folder can be downloaded from https://smu.box.com/s/i2454jb9kpua8hw37ycdxw7codho5p2t
Replace python with path_to_EDHB/EDHB for executing with binary
If secondary structure specification is required (annotation of alpha, beta, turn etc.), download ss.txt from https://smu.box.com/s/ncs1vzhhqn1dy92w2q1te6zq97g614ks and place the file in either EDHB directory (for using with binary) or scripts directory (for python based execution)
INSTALLATION
Go to scripts directory (or EDHB for binary)
- Open main_input
- Point path to local mode if present
- Point path to babel (required)
BASIC SYNTAX
python path_to_scripts/hbond_out.py filename.extension
extension can be any babel compatible file such as pdb, mol2, xyz, pdbqt, fchk etc.
PARAMETERS
The following parameters can be provided for external calculations
Parameters that require no external file
1) -c to include C-H...O bonds
2) -l for local mode calculation from .fchk file generated from gaussian
3) -f for local frequency calculation from .fchk file generated from gaussian
4) -Charg for charges from .fchk file generated from gaussian (Mulliken charges)
5) -R to do Intramolecular analysis
6) -a to add HB angle
7) -B to add bifurcation type (hydrogen bond network)
Parameters that require additional files
1) -Hl hessian_file
hessian_file should have the first line as comment followed by upper triangle of hessian
hessian can have line breaks, however, should be space separated
Check examples/external_hessian/hessian for an example input
2) -d AIMALL_file
AIMALL_file that contains information about Bond Critical Points (BCP) (.sum, .sumviz, .mgpviz etc.)
3) -C NBO_file
NBO_file is the output for an NBO analysis from gaussian
The parameter adds NBO charges to participating hydrogen bond atoms
4) -LP NBO_file
NBO_file is the output for an NBO analysis from gaussian
The parameter adds lone pair contributions
5) -db pdb_id
pdb_id is the ID for a protein taken from Protein Data Bank
The parameter adds secondary structure informations
EXAMPLES
-
water_cluster
python path_to_scripts/hbond_out.py cluster.fchk -d cluster.mgpviz -LP cluster.g09.out -C cluster.g09.out -l –f -
Proteins
python path_to_scripts/hbond_out.py 1k43.pdb –db 1K43 –R –B -
External Hessian
python path_to_scripts/hbond_out.py xtbopt.xyz -Hl hessian -l -f