Relative Binding Free Energy Calculation of Protein-Ligand Complex

User discussions
1

GROMACS version: 2022.3
GROMACS modification: No
Dear GROMACS Community Forum,

I would like to compute the relative binding free energy change of the protein-ligand complex using Thermodynamic Integration method. Is there any tutorial for using TI method of Protein-ligand complex ?
Your suggestions would be highly appreciated.

Thanks &Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana, India

2

I did not find any direct tutorial for this, but you can do by seeing the literature. There are some small tutorials in other packages and in weblinks.

3

I have been looking for the same tutorial. There doesn’t seem to be any simple tutorial for relative binding calculations using TI. I have only been able to find absolute binding free energy tutorials. I haven’t found anything in the GROMACS documentation, Tutorials · GitLab, or the alchemistry wiki. The Lemkul tutorials (GROMACS Tutorials) also don’t have anything for this specific case. Please let me know if you find anything!