Hi Dear Amber users,
I would like to calculate delta free energy value between a ligand and its receptor, for this purpose I performed only one MD simulation for my complex (ligand + receptor) and then I submitted its trajectory frames into the MM_PBSA.py script to obtain binding free energy value, am I in a correct way? because in literatures I often saw that 3 MD simulations were needed for this kind of calculations (i.e, ligand, receptor and complex).
I would be grateful for any advice from your site.
Sincerely,Berk
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Received on Mon May 04 2015 - 11:30:10 PDT
