Re: [AMBER] Topology files of homodimer-ligand complex

From: Jason Swails <>
Date: Thu, 05 Dec 2013 10:20:20 -0500

On Fri, 2013-11-29 at 16:02 -0300, George Tzotzos wrote:
> I'm dealing with a homodimer, in which the ligand is adjacent to the interface between the two monomeric subunits. I want to conduct an MD simulation to (a) find out atomic interactions; (b) find out the binding energy of the ligand (this is to be compared to the one I obtained by running simulations on the monomer).
> My question is the following. In preparing the ligand, protein and complex topology files, is it legitimate to consider the two monomeric subunits PLUS one of the ligands as the PROTEIN? Alternatively, could I construct the complex by renaming one of the ligands and appending both ligands to the protein (homodimer)?

I'm not quite sure what you're asking here. Are you talking in an
MM/PBSA framework? If so, you can treat whatever you want as the
'receptor' and 'ligand', and the resulting energy difference will be (an
approximation to) the binding energy between what you designated as your
'receptor' and what you designated as your 'ligand'.

I'm not sure why you would ever have to change the residue name of any
part of your system (you certainly wouldn't have to for One
caveat: if you have multiple ligands that have the same name, the
default mask assignments in will pick the *last* ligand as the
'ligand' when preparing the files (it will print out the masks it used
for the receptor and ligand). If you want a different ligand chosen,
you will need to specify the receptor_mask and ligand_mask in your input file (&general section).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 05 2013 - 07:30:03 PST
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