On Mon, May 11, 2020, Marcelo Andrade Chagas wrote:
>
>I did simulations of: (APO protein), (protein-lingand-1) and
>(protein-ligand-1-ligand-2).
>
>Successfully performed MMPBSA calculations on the DM trajectory of the
>protein-ligand-1 system, using the single-trajectory procedure.
>
>However, for the ternary system (protein-ligand-1-ligand-2) would it be
>possible to make the calculations the second ligand?
What calculation to you want to do? That is, what free energy change
would you like to estimate? You could define (protein-ligand-1) as the
receptor, (ligand-2) as the ligand, and the whole thing as the complex.
That would attempt to compute the free energy of binding of ligand2 once
ligand1 is already bound.
....dac
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Received on Mon May 11 2020 - 05:00:03 PDT
