We would like to note here that even though MM-GBSA is often called an end-point binding free energy protocol, in our opinion, MM-GBSA scores are better regarded as scores rather than true free energies. The calculations are done on end-point trajectories and use a quasi-harmonic approximation to account for the entropy of the protein and the ligand. Also, the waters in the binding pocket are treated as a continuum solvent and hydrogen-bonds formed by water molecules in the binding pocket are neglected in the calculations.