AMOEBA-Ions: improved description of high field polarization for interactions of proteins with monovalent cations

Abstract

The reliability of molecular mechanics simulations to predict ion binding to proteins depends on their ability to describe accurately both ion-protein and ion-water interactions. Ion parameters are typically constructed using reference data on ion-water interactions. Many studies show that this strategy produces large errors in ion-protein interactions. Studies also show that this transferability error can be corrected to some extent by assigning separate sets of non-bonded cross-terms for every distinct pair of ion type and its coordinating protein functional group.