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Validation of AMBER/GAFF for Relative Free Energy Calculations

preprint
submitted on 02.02.2019, 20:29 and posted on 04.02.2019, 20:08 by Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.
We computed relative binding free energies using GPU accelerated Thermodynamic Integration (GPU-TI) on a dataset originally assembled by Schrödinger, Inc.. Using their GPU enabled free energy code (FEP+) and the OPLS2.1 force field combined with REST2 enhanced sampling approach, these authors obtained an overall MUE of 0.9 kcal/mol and an overall RMSD of 1.14 kcal/mol. In our study using GPU-TI of AMBER with the AMBER14SB/GAFF1.8 force field but without enhanced sampling, we obtained an overall MUE of 1.17 kcal/mol and an overall RMSD of 1.50 kcal/mol for the 330 mutations contained in this data set.

Funding

GM107485

History

Email Address of Submitting Author

songlin3@msu.edu

Institution

Michigan State University

Country

United States

ORCID For Submitting Author

0000-0002-1854-5215

Declaration of Conflict of Interest

no conflict of interest

Version Notes

Version 1 --- Feb.02/2019

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in Journal of Chemical Information and Modeling

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