Re: [AMBER] Luck or Black Box

From: manoj singh <>
Date: Fri, 31 Dec 2010 00:40:11 -0500

Once you have metal at binding site, most likely you have to use (NOE)
restraint and in that case, you can't simply perform MM-PB(GB)SA

It is a very common practice to report structural details (or P value) along
with the free energy calculations.

On Thu, Dec 30, 2010 at 11:55 PM, Eliac Brown <> wrote:

> Dear AMBER
> One of my projects is dealing with the binding affinity calculation of some
> ligands with a certain protein.
> When I calculated the binding energies using MMPBSA, I got a good
> correlation with the experimental data, but when I analyzed the simulation
> trajectory, I found the binding mode of the ligand with the receptor is not
> correct for most of the studied ligands comparing to the crystal structure
> according to the binding mode with the metal ion at the active site.
> I repeated the calculation again (using on modified parameters for the
> metal ion), I got a very good trajectory comparing to the crystal
> structural. But the binding energies were horrible.
> So how does it give good correlation with giving wrong binding mode with
> the active site? It is a luck or a black box.
> Thanks and happy new year
> Eliac
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Received on Thu Dec 30 2010 - 22:00:05 PST
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