Hello! I need to calculate the free energy of complex formation between protein A and ligand B. I am about to simulate in solution the molecular dynamics of A, B and AB complex separately and calculate the free energy of each system using g_lie. Then, I suppose, deltaG = G(AB) - (G(A) + G(B)). Is it a correct algorithm? Or maybe it's better to use "slow-growth" method (whith lambda = 1 for the absence of ligand in the binding pocket) to calculate the difference between G(AB) and G(A)? Thank you!
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