Hi,
Which version of cpptraj are you using? In addition to the good
comments already made, I'll add that GIST has had lots of improvements
over the past few years, including the recent addition of PME to the
energy calculation. If you aren't already, I recommend trying with the
GitHub version (
https://github.com/Amber-MD/cpptraj); see if that
helps.
-Dan
On Wed, Sep 8, 2021 at 12:24 PM Reyes Nuñez Franco <rnunez.cicbiogune.es> 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 don’t 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).
>
> Let’s imagine the simplest case: two different proteins (binding site practically identical) bound to a ligand (the same one for both systems).
>
> I don’t 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 Núñez Franco (PhD student)
>
> CIC bioGUNE
>
>
>
>
>
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Received on Fri Sep 17 2021 - 10:30:03 PDT
