Development of a Parametrized Force Field To Reproduce Semiempirical Geometries.

ABSTRACT

Here we describe the development of a classical force field parameter set to reproduce the geometry of proteins minimized at the semiempirical quantum mechanical level. The overall goal of the development of this new force field is to provide an inexpensive, yet reliable, method to arrive at geometries that are more consistent with a semiempirical treatment of protein structures. Since the minimization of a large number of protein structures at the semiempirical level can become cost-prohibitive, a "preminimization" with an appropriately parametrized classical treatment could potentially lead to more computationally efficient methods for studying protein structures through semiempirical means. Here we demonstrate that this force field allows for more rapid and stable geometry optimizations at the semiempirical level and can aid in the adoption of quantum mechanical calculations for large biological systems.