The solvated and parametrized systems were then further prepared for SepTop using a set of python scripts. Python scripts for performing these operations are currently housed in the GitHub repository SeparatedTopologies, which is under active development. This package contains multiple python scripts that can be used to generate all necessary input files for running SepTop in GROMACS, namely • a coordinate file with the solvated protein-ligand complex having both ligands in the binding site,