Theoretical and Computational Chemistry

Validation of AMBER/GAFF for Relative Free Energy Calculations

Authors

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.

Version notes

Version 1 --- Feb.02/2019

Content

Thumbnail image of GPU-TI_ms_Feb.01_Lin.pdf

Supplementary material

Thumbnail image of Trend.xlsx
Trend
Thumbnail image of GPU-TI_NVT-ddG-SI.xlsx
GPU-TI NVT-ddG-SI
Thumbnail image of FEP_vs_GTI-dG-SI.xlsx
FEP vs GTI-dG-SI
Thumbnail image of Perturbation graph-SI.pdf
Perturbation graph-SI