Calculations of the φ -ψ Conformational Contour Maps for N-Acetyl Alanine N'-Methyl Amide and of the Characteristic Ratios of Poly-L-alanine Using Various Molecular Mechanics Forcefields

Abstract We generated φ -ψ conformational energy contour maps for the of N-acetyl alanine N'-methyl amide using the molecular mechanics forcefields AMBER, AMBER3, BI085, CFF91, CVFF, MM2, MM3, MM+, and SYBYL. With MM2, MM3, and MM+, we used a dielectric constant of ϵ = 1.5, the default effective value for these forcefields. With the other forcefields we used ϵ = 1 and 4, except with SYBYL, which, in Spartan 3.1, has no electrostatic term. All forcefields yielded the Ceq 7 conformation as a low-energy minimum or the global minimum. Most of the forcefields also yielded a minimum-energy conformation in the C5,αR, and αt. regions of the φ -ψ contour map. Fewer of the forcefields yielded a minimum in the Cax 7 region; however, adiabatic relaxation frequently lowered the relative energy of this region. Based on the appearance of the φ -ψ maps, the following pairs of forcefields were broadly similar (but not identical) to each other but dissimilar to the other pairs: AMBER3 and AMBER, BI085 and CHARMM, MM+ and M...