Dear Reyes,
I still think that a value of 125576000 is not expected. However, it is
hard to say why this happens. I assume that this value was obtained
after stripping the ions from the simulation box?
Regarding the ions, the original formulation of IST assumed that there
is only one solvent species. The same is true for the existing GIST
implementations. If you have a significant number of ions in your
system, I am skeptic whether the results would be correct. Specifically,
by stripping the ions you remove interactions from your system which
might be relevant. If you include them you get the problems with Esw
that you mentioned, and it might also mess up the entropy calculation.
As it happens, we are currently working on an extension of GIST that can
take the ions into account (paper submitted). While the manuscript is
not yet on the internet, I could help you try it out if you want. We use
a Python implementation for the ion entropy, and updated GIGIST so that
the ions don't mess with the entropy calculation. If you don't have many
ions in your system, you would not need the entropy. Then you could just
use the updated GIGIST, and use a slightly more complicated referencing
for Eww. The updates are currently in a pull request on
github.com/liedllab/gigist. But if the high values also occur after
stripping the ions, there must be some other problem anyway.
If you cannot figure out why the high values are occurring, you could
send your input files, or I could offer to discuss it via Zoom (both
assuming that the system you are working on is not secret).
Best regards,
Franz
On 9/13/21 12:23 PM, Reyes Nuñez Franco wrote:
> Dear Franz,
>
> Thanks a lot for your answer. In fact, in view of the data values you reported to be normal in your case, I double-checked everything and I realized that the high values I was obtainted were not for "Esw" but for "Eww" (both absolute and normalized).
>
> I've been trying different GIST options and in fact you can obtain extremely high values for the Esw, but just if you do not remove the ions of your trajectory (as it is actually mentioned in the manual). Hence, if ions are not stripped from the trajectory file before running GIST through cpptraj, they are considered as part of the solute and you get that crazy numbers.
>
> However, the question of whether the very high numbers I get for Eww are expected or not is still open...
>
> Thanks again,
> Best,
> Reyes
>
>
> -----Mensaje original-----
> De: Franz Waibl <franz.waibl.uibk.ac.at>
> Enviado el: 09 September 2021 10:46
> Para: amber.ambermd.org
> Asunto: Re: [AMBER] GIST question
>
> CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
>
>
>
> 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 Å, and 0.5 Å 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 Nuñez 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 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 Tue Sep 14 2021 - 10:30:03 PDT
