AMBER-based hybrid force field for conformational sampling of polypeptides

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.