Re: [AMBER] GIST question

From: Franz Waibl <franz.waibl.uibk.ac.at>
Date: Thu, 9 Sep 2021 10:46:05 +0200

Dear Reyes,

An Esw-norm value of 125576000 is pretty strange, especially if it is in
a high-density region. For instance, in one of my GIST calculations, the
Esw values ranged from -27.7 to 10.8. You should double check whether
this value is correct, and whether you get the same value with a
different version of the GIST code (i.e.: different cpptraj version, or
the PME-GIST or GIGIST implementations). Which force field / water model
are you using?

Regarding the values for consecutive voxels, it is expected that they
can have different energy values. The default grid spacing for GIST is
0.5 Ň, and 0.5 Ň can have a large impact on the water energy, especially
at the protein surface.

Sorry if this doesn't really answer your questions. I figured I'd reply
anyway since the GIST user-base is rather small. I have worked with GIST
a lot, but mainly used ff14SB and TIP3P, and didn't ever notice such
high Esw values.

Best regards,

Franz

On 08.09.21 18:24, Reyes NuŮez Franco wrote:
> Dear Amber users,
>
>
> I am using GIST to analyze the structure and thermodynamics of water in the vicinity of the binding site of a complex (protein:ligand complex). I wanted to analyze the solvation differences in complexes formed by different proteins (with a very similar Carbohydrate Recognition Domain) bound to the same ligand.
>
> I was able to do it and visualize different properties but still, there are some things I donít fully understand.
>
> I represented the gist-g0.dx file. In order to assign some properties to the more localized water bridge regions, I treated the gist.out file. I ordered it based on the g_O values (higher to lower).
>
> Letís imagine the simplest case: two different proteins (binding site practically identical) bound to a ligand (the same one for both systems).
>
> I donít understand why for one of the systems the voxels with higher g_O values (top 30) are characterized by an Esw-norm ranging from -2.1 to -0.15 and an Eww-norm ranging from -0.15 to 0.46. However, for the other system, the voxels with higher g_O values are characterized by an Esw-norm ranging from -1.24 to 125576000 and an Eww-norm ranging from -0.10 to 0.30.
>
> Could someone help me understand these numbers? Conditions for the GIST calculations are exactly the same. What is more curious, there are cases in which two consecutive voxels (pointing to the same water region), display so different Esw-norm values (boxel 43573, Esw-norm=946.391 vs boxel 43572, Esw-norm = -0.128).
>
> I would really appreciate if some experts in the field could help me.
>
> Thanks in advance!
>
> Best,
>
> Reyes
>
>
>
>
>
> Reyes NķŮez Franco (PhD student)
>
> CIC bioGUNE
>
>
>
>
>
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