Overall, these arguments highlight the sensitivity of docking to receptor conformation, and motivate the inclusion of flexibility into the receptor , not only for the improvement of docking methodology by itself, but also for providing better docked poses for free energy calculations. In this study, we looked at two different parameters for the MM-GBSA calculations, namely protonation state and protein conformation during our retrospective analysis. Both of these parameters turned out to have non-trivial impact on the calculated binding affinities. However, they are many more MM-GBSA calculation parameters which can possibly affect the binding affinities which were not explored in the current work.