Validation of AMBER/GAFF for Relative Free Energy Calculations

04 February 2019, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

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.

Keywords

AMBER
AMBER18
AMBER14SB/GAFF1.8
GPU TI
TI
FEP+/OPLS2.1
Relative binding free energy
Validation

Supplementary materials

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Trend
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GPU-TI NVT-ddG-SI
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FEP vs GTI-dG-SI
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Perturbation graph-SI
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