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Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field

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Abstract

All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of small molecules as part of the SAMPL4 challenge. Compounds were parametrized on the basis of the OPLS-AA force field using three different protocols for deriving partial charges: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms and derivation of new parameters for a number of distinct chemical groups (N-alkyl imidazole, nitrate) that were not present in the published force field; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian09 at the HF/6-31G* level), followed by two-stage RESP fitting. The absolute hydration free energy was computed by an established protocol including alchemical free energy perturbation with thermodynamic integration. The use of standard OPLS-AA charges (protocol 1) with a number of newly parametrized charges and the use of histidine derived parameters for imidazole yielded an overall root mean square deviation of the prediction from the experimental data of 1.75 kcal/mol. The precision of our results appears to be mainly limited by relatively poor reproducibility of the Lennard-Jones contribution towards the solvation free energy, for which we observed large variability that could be traced to a strong dependence on the initial system conditions.

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Acknowledgments

B.I.I.’s laboratory is a member of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from French National Research Agency (ANR-10-LABX-33).

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Authors and Affiliations

  1. Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ, 85287-1504, USA

    Oliver Beckstein

  2. Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif-sur-Yvette, Labex LERMIT, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France

    Anaïs Fourrier & Bogdan I. Iorga

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  1. Oliver Beckstein
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Beckstein, O., Fourrier, A. & Iorga, B.I. Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des 28, 265–276 (2014). https://doi.org/10.1007/s10822-014-9727-1

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