Introduction to protein ligand free energy calculations (FEP and FEP+)

User discussions
1

Dear, a pleasure to greet you. I am starting to calculate protein-ligand free energy. I have been reviewing many papers, but I can’t find a tutorial or protocol that I can follow step by step and adapt it to my system to do FEP or FEP+ in GROMACS, please, if you can guide me, I thank you very much,

stay tuned,

greetings,

Pablo

2

Welcome to the forum. Firstly, do you want to calculate absolute or relative binding free energies?

I don’t know of any step-by-step binding free energy tutorials. If you are interested in absolute binding free energy calculations, good starting points would be Free energy of solvation — GROMACS tutorials https://tutorials.gromacs.org documentation and Free Energy Calculations. pmx is, as far as I know, more focused on relative binding free energy applications, but can almost certainly be of interest. Also, if you have not yet read AlchemistryWiki, that might also be useful.