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. Author manuscript; available in PMC: 2013 Jan 1.
Published in final edited form as: Wiley Interdiscip Rev Comput Mol Sci. 2011 Jun 28;2(1):167–185. doi: 10.1002/wcms.74

Figure 3.

Figure 3

Illustration of model compounds used in the parametrization of the CHARMM additive protein force field. (a) N-methyl acetamide is used to model the peptide bond; (b) sidechains, such as in PHE, are modeled by analogous compounds that include terminating methyl or ethyl groups; (c) alanine dipeptide is the model compound for optimization of the ϕ/ψ torsional parameters including CMAP corrections.