The ambition of this collaborative report was to evaluate only the binding affinity prediction accuracy of MM-GBSA scores relative to AutoDock4 scores. Therefore, starting with the same binding poses generated using AutoDock-GPU, we compared our predicted affinities with the experimental affinities for the two scoring approaches -AutoDock4 scores and MM-GBSA scores. Based on the correlation statistics and performance metrics obtained for both submissions, we found that re-scoring the affinities using MM-GBSA free energy estimates did not improve the correlation with experimental values. During post-analysis, we found that MM-GBSA scores depend on the initial protein conformation, the protonation states of the BACE-1 active site, and the charge of the ligands, and we were able to improve our MM-GBSAbased correlation metrics retrospectively.