Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?
I used Enzyme Design application to get a series of enzymes with ligand(transition state of my target reaction). Now I want to inspect the free energetic change upon the protein transition state binding.
So I first look into the ddg_monomer application, and I find this application is suitable for comparing ddg energy between wild-type protein and its mutant structures. This can't meet my needs.