AMBER-based hybrid force field for conformational sampling of polypeptides

Abstract

AMBER-based hybrid force field was developed, with mixing the mainchain torsion energies of AMBER parm94 and parm96 force fields, with introducing a weighting factor to control the mixing ratio. First, dependence of an adiabatic Φ– Ψ potential–energy map of alanine dipeptide on the weighting factor was investigated, and the map was compared with an ab initio Φ– Ψ map. Second, we did enhanced conformational sampling of two six-residue peptides known to form a helical or turn conformation in solution. The hybrid force field reproduced the ab initio energy better than either parm94 or parm96, and exhibited the secondary-structure preference depending on the amino acid sequence.