Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field
Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed point charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard, but showed substantially worse results than those using the fixed point charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 dataset, we evaluate the cumulative effects of a series of incremental improvements in parameterization protocol, including both solute and solvent model changes. Ultimately the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein ligand binding studies
3871-3883
Bradshaw, Richard T.
a13f4a6d-2f1b-4194-98e4-818aa1d250ef
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
29 July 2016
Bradshaw, Richard T.
a13f4a6d-2f1b-4194-98e4-818aa1d250ef
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Bradshaw, Richard T. and Essex, Jonathan W.
(2016)
Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field.
Journal of Chemical Theory and Computation, 12 (8), .
(doi:10.1021/acs.jctc.6b00276).
Abstract
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed point charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard, but showed substantially worse results than those using the fixed point charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 dataset, we evaluate the cumulative effects of a series of incremental improvements in parameterization protocol, including both solute and solvent model changes. Ultimately the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein ligand binding studies
Text
Bradshaw_Amoeba_HFE_postreview.pdf
- Accepted Manuscript
Text
acs.jctc.pdf
- Version of Record
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Accepted/In Press date: 24 June 2016
e-pub ahead of print date: 24 June 2016
Published date: 29 July 2016
Organisations:
Computational Systems Chemistry
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Local EPrints ID: 398612
URI: http://eprints.soton.ac.uk/id/eprint/398612
ISSN: 1549-9618
PURE UUID: 0f9d88bd-55e2-4a9e-9b2d-b5175cdd2b8a
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Date deposited: 29 Jul 2016 11:27
Last modified: 15 Mar 2024 05:46
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Author:
Richard T. Bradshaw
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