| Abstract
| - The generalized Born model proposed by Still and co-workers (Qui, D.; Shenkin, P. S.; Hollinger, F. P.;Still, W. C. J. Phys. Chem. A1997, 101, 3005−3014) is parametrized specifically for proteins, peptides, andnucleic acids within the CHARMM all hydrogen and polar hydrogen force fields. A database of atomicelectrostatic environments and molecular electrostatic solvation free energies comprising amino acid residues,nucleic acid bases, dipeptides, dinucleotides, proteins, and DNA strands is established, and numerical finitedifference Poisson calculations are solved using atomic radii and charges from the corresponding force fieldparameters. These data provide the necessary input to parametrize generalized Born models for a particularforce field. The performance of these models in reproducing overall molecular solvation trends is examinedand found to be quite good. Furthermore, calculations of electrostatic solvation free energy differences suggestthat conformational free energy changes are well reproduced. Finally, the utilization of this generalized Bornmodel in molecular dynamics simulations (both with and without cutoffs) is shown to give excellent agreementwith explicit solvent simulations of a small 56-residue protein in water.
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