Re: [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2

From: David A Case <>
Date: Mon, 11 May 2020 07:55:47 -0400

On Mon, May 11, 2020, Marcelo Andrade Chagas wrote:
>I did simulations of: (APO protein), (protein-lingand-1) and
>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.


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Received on Mon May 11 2020 - 05:00:03 PDT
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