Re: [AMBER] Energy contribution of phosphorylated residues

From: Kenneth Huang <>
Date: Thu, 18 Jun 2015 12:06:25 -0400


I think so- someone might be able to give a more detailed answer than me,
but if you have MMPBSA decompose the binding energy by a per residue basis,
you'll be able to estimate their relative contributions. That said, you'll
may want to have it decompose all residues if you can, and run the
hetrodimer without the phosphoserine present so you can have a point of
comparison to see how it contributes.

A more general example off the top of my head is it is fairly dated and there's
probably much more recent work done since that would be worth looking into.



On Thu, Jun 18, 2015 at 9:57 AM, Parker de Waal <>

> Hi Everyone,
> I'm currently working with a heterodimer protein complex in which one
> protein is phosphorylated and this interaction has been shown in vitro to
> be required for dimer formation.
> Using MM/PBSA, would it be possible to perform an energy deconvolution to
> determine the energy contribution of the phosphoserine and the two salt
> bridges it is forming?
> I am familiar with protein-ligand calculations, but in this case it is
> protein-protein.
> Any advice would be greatly appreciated.
> Best,
> Parker
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Received on Thu Jun 18 2015 - 09:30:04 PDT
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