Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.