Development and testing of new force fields for molecular dynamics simulations

Abstract

Recent progress in modeling of protein folding in Dr. Shaw laboratory has been achieved only after some improvements of potentials of covalent forces, taken from the standard AMBER force field; and still, the force field used is not quite satisfactory to reproduce folded structures of some larger proteins, having significant, about 5A, RMS deviation between the computed and experimentally determined 3D structures. The objective of this research is to develop and test new polarizable atomic force fields (FFs) for "in-vacuum" and "in-water" non-bonded interactions based on AMBER ff99SBILDN force fields, improved by inclusion of new terms. FFs parameter optimization will be done using our set of molecular crystals with crystallographic data from the Cambridge Structural Database and sublimation/solvation thermodynamics characteristics from various sources.