Given the hostguest.pdb file containing the receptor (βcyclodextrin) and the ligand molecule, we will obtain separate PQR files for the receptor and ligand molecule, respectively. These files are required to run BD simulations to calculate the receptor-ligand binding rates (kon). To obtain the PQR files, we will use the ambpdb program integrated into the Ambertools. The ambpdb program requires a topology file (hostguest.parm7) and a coordinate file (hostguest.inpcrd) to create a PQR file (hostguest.pqr). The PQR file is almost identical to a PDB file, except the charge and radius columns in the PQR files substitute the beta and occupancy columns in the PDB file. Once a hostguest.pqr file is created using the ambpdb tool, we want to create two separate PQR files from the hostguest.pqr file, i.e., the receptor.pqr file containing the coordinate, charge, and radius information of the receptor atoms and the ligand.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., hostguest.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., hostguest.pqr by executing the following command: The script then further creates receptor.pqr and ligand.pqr files by reading into the hostguest.pqr file. To achieve this, we execute the following command in the terminal: