Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding

From: Jason Swails <>
Date: Sun, 17 Nov 2013 11:33:43 -0500

On Sun, Nov 17, 2013 at 12:03 AM, Vaibhav Jain <>wrote:

> Hello everyone !!
> I am wondering if MM-PBSA approach can be used for calculating the binding
> free energy of a ligand with a macromolecule in the presence of other bound
> identical ligands, which are in close proximity or stacked together.

Sure. How you proceed depends on what you want to learn. You can treat
one ligand as the 'ligand' and the rest as part of the 'receptor'. You can
treat all ligands as one collective 'ligand' and the receptor as the
receptor. The first approach is probably more reliable than the others
(especially if there is cooperativity in the different binding events
associated with conformational allostery).

System consisting of hyperbranched polymer in which 7 molecules of same
> ligand are encapsulated. Now I wish to calculate the binding free energy of
> each of the 7 bound ligand.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 17 2013 - 09:00:02 PST
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