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RESEARCH PRODUCT

Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

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Abstract The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH2 backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The γ global and the α, β and Δ local minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or over-estimate the relative energy of some local minima, the ID polarization energy term represents a significant correctio...