Abstract
A protocol for computing absolute binding free energies with the AMOEBA polarizable force field is presented. Examples discussed include various host-guest complexes from the SAMPL community exercises, binding of ions to an RNA G-quadruplex and a series of protein-ligand interactions. In many cases where calculations are not limited by sampling issues, the AMOEBA model is able to provide binding values within “chemical accuracy,” i.e., roughly 1 kcal/mol from experiment.
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