Re: [AMBER] MMPBSA- topology files preparation

From: Jason Swails <>
Date: Mon, 23 May 2016 08:57:44 -0400

On Sat, May 21, 2016 at 10:44 PM, Kat G <> wrote:

> Hi all,
> I am interested in MMPBSA estimation for the interaction of protein and
> ligand. My system is a homo-dimer, and each monomer interacts with the same
> ligand at Mg2+ site. By experiments, we know that only in dimer form and
> with the presence of Mg2+ cofactor, ligands can be bound to the dimer
> structure. Then my question is how should I prepare topology files for
> "receptor" and "ligand" in this case for meaningful calculation.
> 1. "Ligand" is ligand 1, and "receptor" is a dimer, 2 Mg2+ ions, and the
> other ligand. Then "complex" is the whole system, except WAT and
> counter-ions.
> 2. "Ligand" is both similar ligands, and "receptor" is a dimer with Mg2+
> ions.
> 3. "Ligand" is ligand 1, and "receptor" is just one corresponding monomer
> and Mg2+ ion. Then, complex is just only 1 monomer interacting with 1
> ligand.
> Could it be one of these above cases? I think of the first case but still
> not be sure. Could you please give me any suggestion.

​They are all valid choices depending on what you are trying to learn.


Jason M. Swails
AMBER mailing list
Received on Mon May 23 2016 - 06:00:06 PDT
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