Re: [AMBER] Help with GIST analysis

From: Steven Ramsey <>
Date: Wed, 19 Oct 2016 16:56:41 -0400

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,


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
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Received on Wed Oct 19 2016 - 14:00:03 PDT
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