New methods for potential functions for simulating biological molecules

We use the CM1A class IV charge model and the SM5.4/A and SM.5.4PD/A solvation models to calculate atomic charges and solvation energies for 9-methyladenine and thymine and for alanine and serine dipeptides. The CM1A quantum mechanical charge model provides atomic charges as accurate as or more accurate than those used in popular molecular dynamics force fields but is very economical in both computer time and effort required to generate charges; thus it is very promising for examining effects of conformational changes, substituents, solvation, binding, and even reaction. The solvation models have been parameterized over multiple functionalities and are well suited to rapid calculations on large systems.