Many previous studies have evaluated the ability of molecular mechanics combined with the Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics combined with generalized Born surface area (MM-GBSA) methods to predict ligand binding poses and binding affinities, and compared the accuracy of these predictions to that of docking scores . Kaus et al. have reported that MM-GBSA method performs better than standard scoring functions in ranking binding poses. Similarly, Rastelli et al. have shown that both MM-GBSA and MM-PBSA rescoring methodologies improve the affinity ranking estimated by AutoDock scoring function.