I’ve run a 100ns MD trajectory of a receptor liganded to two identical ligands.
My objective is to determine the relative binding energies of the ligands.
I’ve stripped the trajectory of water molecules, ions and ligand_1, prepared new topology files and performed MMGBSA.
I repeated the above process leaving in the complex ligand_1 and stripping ligand_2.
Is this approach legitimate?
Looking forward to your advice and comments
Regards
George
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Received on Mon Feb 16 2015 - 12:00:03 PST
