MM-PB-GB-SA_Benchmarks

"MM/PB(GB)SA Benchmarks on Soluble Proteins and Membrane Proteins"

Overview

This library contains:

1. Molecular structures of the article "MM/PB(GB)SA Benchmarks on Soluble Proteins and Membrane Proteins" in Membrane and Water_soluble folders,
2. A tutorial and essential files of "Obtaining a gromacs topology with an off-center charge" are in Add_EPs file.
3. Example of R and MAE calculation is in R_MAE.

Dependencies

• AmberTools: https://ambermd.org/AmberTools.php
• Gaussian software: https://gaussian.com/
• CGenFF Tool: https://cgenff.umaryland.edu/

Tutorial

See Add_EPs

Reference

Costa, P. J. (2021). Transmembrane Anion Transport Mediated by Halogen Bonds: Using Off-Center Charges. Computational Design of Membrane Proteins. I. S. Moreira, M. Machuqueiro and J. Mourão. New York, NY, Springer US: 273-284.

Wang, L., et al. (2015). "Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field." Journal of the American Chemical Society 137(7): 2695-2703.