Re: [AMBER] Help with GIST analysis

From: Sérgio Marques <>
Date: Thu, 20 Oct 2016 11:18:02 +0200

Dear Steve,

Thank you for your replying and for such extended explanation!

You might be right about the box size and the possible effects on other
layers of solvation. However, for some systems I have tried a box covering
almost the whole system (70 A box, which took weeks to calculate), but I
also didn't observe what I expected (the mutant with increased water
Regarding the energies, I will try to put a threshold on the enthalpy and
recalculate the parameters, and then maybe recalculate the GIST without
aligning the systems.

Thanks again!!

Best regards

Sérgio Marques, PhD

Marie Curie Fellow at:
*Loschmidt Laboratories*
Department of Experimental Biology
Faculty of Science, Masaryk University
Kamenice 5/A13, 625 00 Brno, Czech Republic

On 19 October 2016 at 22:56, Steven Ramsey <> wrote:

> Hi Sergio,
> That sounds like a really interesting system!
> You certainly can evaluate solvent energies and entropies utilizing regions
> of interest defined around each residue as you described. One issue to keep
> in mind is whether 15 Å is large enough to capture most of the solvent
> reorganization, if the grid is centered on the COM of a SER residue for
> example it would therefore at most extend 7.5 Å out from the protein
> surface, this distance will include all of the first solvent shell and
> most/all of the second solvent shell, but may not include outer shells. It
> would be important to make sure these regions are large enough to capture
> all of the solvent reorganization within your system, it might be that 15 Å
> is not enough, I would suggest trying different GIST regions and see
> whether that addresses some of your concerns.
> There is a known issue when applying GIST to unrestrained systems that are
> then aligned using rms in cpptraj that produces arbitrarily high energies
> and that sounds to be the issue at hand with your Eww being 1.12E+06. If
> possible you may want to avoid aligning the system prior to running GIST.
> It's hard to say how different the visualization will be between these
> mutants. Keep in mind that .dx visualization is done by a threshold, which
> is to say the mesh or points that you see are the interface between the
> isovalue cutoff that you set. This visual does not tell you which side of
> this threshold is higher or lower, by that I mean you can see two .dx map
> visualizations that look exactly the same but have inverted data of one
> another (so similar visuals can mean entirely different values). I wouldn't
> expect an extreme shift here personally...the sum of the quantities will
> tell the story better, but even small visual differences are likely
> meaningful. Sorry if that explanation of visualization was vague!
> Hope this helps,
> --Steve
> On Wed, Oct 19, 2016 at 11:31 AM, Sérgio Marques <> wrote:
> > Hello,
> >
> > I have one template protein and we have recently discovered several
> mutants
> > with higher stability (e.g. Glu to Ser). This stabilization could not be
> > predicted computationally with any energy-based method (e.g. Rosetta,
> > FoldX, etc.), and we are trying to explain it. After several
> computational
> > studies and experiments, everything points out to the observed
> > stabilization being due to the entropic effects of the solvent, since we
> > failed at predicting any structural stabilization.
> >
> > So I have run GIST calculations on those systems in an attempt to find
> the
> > possibly different entropic contributions from the solvent, but I am
> facing
> > some difficulties in interpreting the results. I ran the GIST on 200 ns
> > long MD simulations and used 4 ns-spaced snapshots, with boxes of 15 A
> > width centered in the mutated residues. The calculations were performed
> on
> > the aligned template protein single-point mutants using exactly the same
> > size and coordinates of the box (so the boxes match exactly in space).
> >
> > My main questions are:
> >
> > - Can I compute the mutant-wild type differences of the total quantities
> > (dTSorient, dTStrans, Esw and Eww) obtained for the box in order to
> explain
> > the different contributions? I tried to do that but it did not provide
> the
> > results I expected. Moreover, for some systems the Eww was huge (e.g.
> > 1.12E+06 kca/mol, while for other systems it was more reasonable, e.g.
> -600
> > kca/mol)
> >
> > - When visualizing the results, the patterns of entropy and enthalpy
> around
> > the target residues are slightly different but not very significantly. I
> > was expecting the paterns with a certain negative isovalue of dTStotal to
> > shift farther away from the mutant. How different patterns should I
> expect
> > for a mutant that has stabilization due to the entropic contribution of
> the
> > solvent?
> >
> > Thank you in advance for any possible help with this matter!!
> >
> > Sergio Marques
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
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Received on Thu Oct 20 2016 - 02:30:03 PDT
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