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Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high‐level ab initio interaction energies

To properly represent weak hydrogen bonds to sulfur in biological systems, a new multipoint model of atomic sulfur for the amino acid methionine is introduced. This is of particular importance for the description of ligand‐protein interactions. The parametrization is performed by fitting the nonbonding parameters of dimethyl sulfide to high level ab initio interaction energy surfaces of the dimethyl sulfide‐methanol system and incorporating them in the GROMACS force field. Two examples demonstrate the performance of the new model, the molecular dynamics simulations of the hRAR receptor and of α‐lytic protease. In hRAR the origin of the discrimination between the R‐ and S‐enantiomers of the synthetic ligand BMS 184394 is explained, and in the simulation of the α‐lytic protease it is shown that no artificial long range disorders are introduced by the new parametrization. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 283–293, 2005