Solvation Free Energy of Biomacromolecules:  Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field

Abstract

The generalized Born (GB) model provides rapid estimates of the electrostatic free energies of solvation for diverse molecules and molecular ions. This method is expected to be of considerable utility for studies of solvation in macromolecular and biological systems. Calculations on biological molecules are typically based on empirical energy functions, each of which have their own prescriptions for determining net atomic charges. For maximum compatibility, GB parameters tailored to specific force fields are required. The development of parameters compatible with the AMBER force field is described. The method is used to estimate free energies of A and B form structures of DNA obtained from molecular dynamics simulations. The results provide an account of the conformational preferences of right-handed DNA in solution.