Development of a Physics-Based Molecular Force Field for Biomolecule Simulations

Physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term, “physics-based,” is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization, rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. First, the suitability of combining the intramolecular interaction term of MM3 and the intermolecular interaction term of the PMFF was evaluated because we adapted MM3 to describe the intramolecular interactions. The conformational energy ...