Protein folding polarizing force fields in ECEPP2 and MM2
The empirical conformational energy program for peptides (ECEPP2) and
molecular mechanics (MM2) are used for the simulation of the For-Gly-NH2
backbone. Two different methods are proposed 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). A comparative study of the force fields ECEPP2 and
MM2+polarization is presented. Molecular mechanics results are discussed,
including the total energy differences, partitional analyses of the total
steric energies and torsion dihedral angles. The global GAMMA and the local
ALPHA, BETA and DELTA minima are stabilized by intramolecular hydrogen bonds.
Although ECEPP2-based calculations rather under or overestimate the relative
energy of some local minima, the ID polarization energy term represents a
significant correction to the total relative energy.