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

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 ?1 and ?2 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.

SUBMITTER: Huang J

PROVIDER: S-EPMC3800559 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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

Huang Jing J MacKerell Alexander D AD

Journal of computational chemistry 20130706 25

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, RDC ...[more]

PMID: 23832629

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

Publications

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

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