Supplemental Information
Extending the treatment of backbone energetics in protein
force fields: limitations of gas-phase quantum mechanics in
reproducing protein conformational distributions in
molecular dynamics simulations
Alexander D. MacKerell, Jr., Michael Feig and Charles L. Brooks, III
Table S1. Crystallographic average phi, psi values for α-helical residues in selected crystal structures as reported in the PDB.
Lysozyme crambin BPTI MbCO 1I27 1BZP
φ
-69.4±16.0
-65.4±11.8
-71.7±17.4
-62.7±8.7 -66.0±9.8 -64.9±7.2
ψ
-36.1±11.4
38.2±9.4
-38.4±10.2
-42.0±8.5 -38.3±8.6 -39.2±7.1
Values were obtained from the Dihedral Angle table under Geometry link for the respective PDB pages for each protein. Errors represent the standard deviations.
Figure S1. Glycine dipeptide φ, ψ energy maps from empirical calculations with A)
CHARMM22, B) MCSA optimized φ, ψ parameters, C) MCSA optimized φ, ψ
parameters with CROSS terms and D) the spline-based energy correction. Energy
