Re: Protein-ligand affinity

From: Aron Broom (
Date: Mon Oct 14 2013 - 22:16:00 CDT

As an FYI, that energy is going to be border-line useless without having an
unbound control to subtract.

You may want to read up on the literature surrounding this, it is a very
large topic, with many nice reviews, and the problem itself is fairly
nuanced. What you seem to be talking about is an MM/PBSA style of
calculation, so I'd start by looking into that.

On Mon, Oct 14, 2013 at 2:20 PM, James Starlight <>wrote:

> Dear NAMD users,
> I have trajectory of the protein complexed with the ligand (burried in the
> protrein interiour from the start of simulation). Now I want to find out
> how I can calculate affinity of my ligand to the protein. The one possible
> way of do such task is the interaction energy estimation of my complex
> (based on the occurence of the non-covalent contacts between both partners
> during production run). Could someone provide me with some tutorial or
> explain me how I could perform such analysis with the VMD tools ?
> Thanks for help,
> James

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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