CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
Article first published online: 6 JUL 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 25, pages 2135–2145, 30 September 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2135–2145. DOI: 10.1002/jcc.23354, .
- Issue published online: 19 AUG 2013
- Article first published online: 6 JUL 2013
- Manuscript Accepted: 26 MAY 2013
- Manuscript Revised: 23 APR 2013
- Manuscript Received: 7 MAR 2013
- NIH (A. D. M.) . Grant Number: GM051501, GM072558
- National Science Foundation . Grant Number: OCI-1053575
- Swiss National Science Foundation Fellowship (J. H.) . Grant Number: PBBSP2_144301
- molecular mechanics;
- empirical force field;
- residual dipolar coupling;
- G protein B1;
- cold-shock protein A;
- fatty acid binding protein
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. © 2013 Wiley Periodicals, Inc.