Abstract: A new set of parameters consistent with AMBER force field for generalized Born model was proposed. The new set of parameters includes the initial radius and screen parameters for 21 atom types. The parameters were developed by fitting the experimental aqueous free energies of solvation of 359 small organic molecules using a genetic algorithm. The derived parameters were then used to predict the solvation free energy of 44 small organic molecules. The calculated results are in good agreement with the experimental values, which are much better than those using the Jayaram’s parameters. Moreover, the derived parameters were then used to predict the solvation free energy of 15 proteins, and the calculated results showed higher linear correlation with those predicted by PB/SA.

Key words: Aqueous free energy of solvation, Solvation effect, Generalized Born model, Poisson-Boltzmann equation