Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field

Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed point charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard, but showed substantially worse results than those using the fixed point charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 dataset, we evaluate the cumulative effects of a series of incremental improvements in parameterization protocol, including both solute and solvent model changes. Ultimately the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein ligand binding studie