[AMBER] MMPBSA- topology files preparation

From: Kat G <katwin86.gmail.com>
Date: Sat, 21 May 2016 21:44:56 -0500

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

2. "Ligand" is both similar ligands, and "receptor" is a dimer with Mg2+

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

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.

AMBER mailing list
Received on Sat May 21 2016 - 20:00:04 PDT
Custom Search