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penev
- Last Updated: 2008-05-29
E. Penev, J. Ireta, and J.-E. Shea (2008)
Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields
J. Phys. Chem. B 112(22):6872--6877.
Abstract
We present a novel method for comparing the long-range part of force
fields in the presence of a maximally cooperative network of nonbonded
interactions. The method is based on mapping the potential energy
surface of an infinite polypeptide chain in the gas phase using
cylindrical coordinates (the twist and pitch) as geometry
descriptors. We apply our method to an infinite polyalanine chain and
consider the AMBER99, AMBER99SB, CHARMM27, OPLS-AA/L fixed
partial-charge force fields and the protein-specific version of the
AMOEBA polarizable force field. Results from our analysis are compared
to those obtained from high-level density-functional theory (DFT)
calculations. We find that all force fields produce stronger
stabilization of the helical conformations as compared to DFT, with
only AMBER99/AMBER99SB satisfactorily reproducing all three helical
conformations (pi, alpha and 3_10).
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A new look at commonly used force fields
