[AMBER] MMPBSA for homo-dimer system with ligands

From: Kat G <katwin86.gmail.com>
Date: Mon, 16 May 2016 00:03:35 -0500

Hi all,

I am interested in MMPBSA calculation for the interaction of protein and
ligand. My system is a homo-dimer, and each monomer interacts with the same
ligand. The question is how should I define "receptor" and "ligand" in this

The first trial, I treated "receptor" as dimer protein and "ligand" as 2
ligands. For the second one, "receptor" is a dimer and 1 ligand, and
"ligand" is the other ligand. Both of these cases give rather big negative
delG_binding values, the second one seems to be a half of the first. But
they are all driven by delG_solvation (big negative number), not delG_gas
(small positive number). Protein-ligand interaction is observed strongly
during MD and experimental data.

I suppose that my definition "for receptor" and "ligand" would cause the
trouble to the MMPBSA calculations. Could anyone give me an advice.

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Received on Sun May 15 2016 - 22:30:03 PDT
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