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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

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    ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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    † ‡ § †Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
    *E-mail: [email protected]. Phone: +1 (631) 632-5424. Fax: +1 (631) 632-5405.
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2015, 11, 8, 3696–3713
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    https://doi.org/10.1021/acs.jctc.5b00255
    Published July 7, 2015
    Copyright © 2015 American Chemical Society
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    Abstract

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    Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.

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    Supporting Information

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    Force field parameter files, additional information about structure generation and filtration and fitting of new side chain dihedral parameters, analysis of side chain scalar coupling convergence, NOE violations divided into backbone–backbone, backbone–side chain, and side chain–side chain restraints, and testing of the AMBER12-bundled ff12SB in comparison with ff14SB presented in the main text. The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.5b00255.

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    Cite this: J. Chem. Theory Comput. 2015, 11, 8, 3696–3713
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