To generate the topology files, the script first inserts the topology of ligand B into the topology of the protein-ligand A complex. Then the [ atomtypes ] section is modified by adding atom types for dummy atoms that describe the non-interacting ligand, as well as "scaled" atom types, where the LJ-ϵ (see Equation ) was scaled down by multiplying the LJ-ϵ by a scaling factor γ. The later atom types were then used for the enhanced sampling protocol, as described below. In addition, the atom type names for the ligand atoms were renamed to produce distinct atom type names for ligand A and ligand B. This was necessary in order to be able to exclude interactions between the two ligands in a next step by defining special non-bonded interactions between atom types. More specifically, the script adds a [ nonbond_params ] section to the topology file in which the vdW interactions between atom types of ligand A and atom types of ligand B are defined as zero.