Professor Alexander D. MacKerell, Jr.
Pharmaceutical Sciences
University of Maryland
Baltimore, MD

Monday, January 28, 2019
3:00 pm (CT)
3269 Beckman Institute

Abstract

The inclusion of the explicit treatment of electronic polarizability in empirical force fields offers the potential to significantly improve the accuracy of molecular simulations of chemical, biological and pharmacological systems in condensed phases. Towards this goal we have developed a polarizable force field based on the classical Drude oscillator model. The Drude force field encompasses proteins, nucleic acids, lipids, carbohydrates and a limited range of drug-like molecules allowing for simulation studies of heterogeneous systems. An advantage of the Drude approach over other methods to model polarization is the inclusion of an explicit particle to model the electronic degrees of freedom allowing for steric contributions associated with electronic polarization to be modeled, a capability that has been used in the Drude Mg2+ ion and halogen parameters. The utility of the model over the additive CHARMM36 force field has been shown in the treatment of the cooperatively of helix formation of the (AAQAA)3 peptide and in the unfolding of Amyloid peptides, on base flipping in DNA and on the interactions of ions with DNA. An overview of the model will be presented along with ongoing developments and applications of the force field.