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Suggested commmand-line use

We recommend using BINANA with the -output_dir parameter, which will save all output files to a specified directory:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_dir /path/to/output/directory/ > errors.txt

If a directory is specified, BINANA creates the following files:

1. Separate PDB files containing the atoms involved in each interaction analyzed.

2. A description of the interactions written to a file called log.txt.

3. Detailed information about the identified interaction saved to output.json and output.csv.

4. A VMD state file (state.vmd) so the results can be easily visualized in VMD, a free program available for download.

To save warnings and errors, append something like > errors.txt to the end of your command.

Alternative methods of use

To output limited information about the detected interactions to the standard output:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt

To create a single PDB file that includes the atoms involved in the identified interactions, with interaction characteristics described in the PDB header:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb

Note that in the above example, errors and warnings are not written to the output file. To save these to a file, try:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb > errors.txt

To output a JSON file with all the characterized interactions between the protein and ligand:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_json /path/to/output.json

To output a CSV file with the same information:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_csv /path/to/output.csv

Specifying custom parameters

Though we recommend using program defaults, the following command-line tags can also be specified: -close_contacts_dist1_cutoff -close_contacts_dist2_cutoff -electrostatic_dist_cutoff -active_site_flexibility_dist_cutoff -hydrophobic_dist_cutoff -hydrogen_bond_dist_cutoff -hydrogen_halogen_bond_angle_cutoff -halogen_bond_dist_cutoff -pi_padding_dist -pi_pi_interacting_dist_cutoff -pi_stacking_angle_tolerance -T_stacking_angle_tolerance -T_stacking_closest_dist_cutoff -cation_pi_dist_cutoff -salt_bridge_dist_cutoff -metal_coordination_dist_cutoff

For example, if you want to tell BINANA to detect only hydrogen bonds where the donor and acceptor are less than 3.0 angstroms distant, run:

python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0

What follows is a detailed description of the BINANA algorithm and a further explanation of the optional parameters described above. Parameter names are enclosed in braces.