A python-based command line script that predicts the sites for non-specific binding of a certain type of ion around a biomolecule using electrostatics and geometrical factors

Python version 3+ is a requirement.

In the command line, type:

python PATH/TO/BION2.py -h

to see the command line options.

To run BION2, one needs a PQR or a PDB file. If PQR file is being used, then DelphiPka need not be run (--nodpka). Otherwise, a CRG, SIZ and topology file along with a PDB file must be provided to obtain a protonated PQR formatted file of the molecule. The protonation can be done at some pH value which can be provided using the --pH flag.