Development and validation of a new force field depending on protein structures for molecular dynamics simulations

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In order to develop a new force field depending on the tertiary structures of proteins, which can be used in classical molecular dynamics simulations, we performed highly accurate quantum chemical computations for typical and stable secondary structures, alpha-helices and beta-sheets (both parallel and anti-parallel conformations). Then, the conformation energies of a variety of the peptide structures were compared with those calculated with AMBER99-SB classical force field. Consequently, for parallel and anti-parallel beta-sheets, the energies given by the classical force field almost agreed with those by quantum chemical calculations. On the contrary, the former energies were much lower than the latter energies for alpha-helices, and alpha-helices were more stabilized as the peptide becomes longer with the classical force field. These deviations in the conformation energies calculated with the classical force field were well compensated depending on the tertiary structures.