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Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

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Abstract

Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.

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Acknowledgments

This investigation has been supported by a grant from the Swedish research council (agreement C0020401). The computations were performed on computer resources provided by the Swedish National Infrastructure for Computing (SNIC) at Lunarc at Lund University and HPC2N at Umeå University.

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Authors and Affiliations

  1. Department of Theoretical Chemistry, Chemical Center, Lund University, P.O. Box 124, 221 00, Lund, Sweden

    Francesco Manzoni & Pär Söderhjelm

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  1. Francesco Manzoni
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  2. Pär Söderhjelm
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Correspondence to Pär Söderhjelm.

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Manzoni, F., Söderhjelm, P. Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field. J Comput Aided Mol Des 28, 235–244 (2014). https://doi.org/10.1007/s10822-014-9733-3

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  • DOI: https://doi.org/10.1007/s10822-014-9733-3

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