Re: Protein-ligand affinity

From: James Starlight (
Date: Tue Oct 15 2013 - 12:42:09 CDT

So in that case just ussage of VMD's NAMD energy module would give wrong
results of the G-bonding estimation.
Also I've found that Free energy perturbation and Thermodynamic integration
could be usefull for affinity measurements. I've seen tutorials for
implementation of such methods for gromacs and charm but is there any for


2013/10/15 Aron Broom <>

> 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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