Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations
We have devised a new efficient approach tocompute combined quantum mechanical (QM) and molecularmechanical (MM, i.e. QM/MM) ligand-binding relative freeenergies. Our method employs the reference-potentialapproach with free-energy perturbation both at the MMlevel (between the two ligands) and from MM to QM/MM(for each ligand). To ensure that converged results areobtained for the MM → QM/MM perturb