Re: [AMBER] Binding deltaG in ligand pose selction

From: David A Case <>
Date: Thu, 21 Jul 2016 11:30:05 -0400

On Wed, Jul 20, 2016, anu chandra wrote:
> I am trying to predict the best binding pose of a ligand to protein. For
> this, I ran short simulations (30-50 ns) of different docked poses of the
> ligand with protein. I just wonder whether a comparison of deltaG binding (
> calculated using will be helpful in identifying the most
> probable binding pose of the ligand?

It's worth a try. Since you already have the simulation, a "single
trajectory" MMPBSA run should be pretty quick and straighforward, and might
provide some new insights. Concentrate on trying to understand the nature
of the interactions rather than "just" getting a binding energy score.


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Received on Thu Jul 21 2016 - 08:30:02 PDT
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