Given the trypsin_benzamidine.pdb file containing the receptor (trypsin) protein and the ligand (benzamidine) molecule, we will obtain separate PQR files for the receptor and ligand molecule, respectively. The ambpdb program requires a topology file (trypsin_benzamidine.prmtop) and a coordinate file (trypsin_benzamidine.inpcrd) to create a PQR file (trypsin_benzamidine.pqr). Once a trypsin_benzamidine.pqr file is created using the ambpdb tool, we would want to create two separate PQR files from the trypsin_benzamidine.pqr file, i.e., the trypsin.pqr file containing the coordinate, charge, and radius information of the receptor atoms and the benzamidine.pqr file containing the coordinate, charge, and radius information of the ligand atoms. The python script, create_BD_files.py generates a coordinate file, i.e., trypsin_benzamidine.inpcrd using the CPPTRAJ module with the structure and topology files as input. Once the coordinate file is generated, the script then creates a PQR file, i.e., trypsin_benzamidine.pqr by executing the following command: