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J Comput Chem. 2013 Sep 30;34(25):2135-45. doi: 10.1002/jcc.23354. Epub 2013 Jul 6.

CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.

Author information

1
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn St., Baltimore, Baltimore, Maryland 21201, USA.

Abstract

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side-chain amino- and methyl-containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ1 and χ2 dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs.

KEYWORDS:

G protein B1; J-coupling; calmodulin; cold-shock protein A; empirical force field; fatty acid binding protein; lysozyme; molecular mechanics; residual dipolar coupling; ubiquitin

PMID:
23832629
PMCID:
PMC3800559
DOI:
10.1002/jcc.23354
[Indexed for MEDLINE]
Free PMC Article

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