Interesting. I have not seen this issue before. What version of
Amber/AmberTools are you using? Have you run the Amber tests that are
provided with the source code? That's where I would start to confirm you
see the same trend again with your Amber.
The energy calculations with MMPBSA.py are actually done by sander, so if
you're consistently seeing these results be off substantially (which it
looks like you are), then I would suggest you re-compiling Amber in serial.
I would also think that the Amber tests for sander would likely fail with
this issue. So you might try running those tests before re-compiling, as
well. Regardless, my guess is that the inherent error is not directly with
MMPBSA.py, but is an issue with one of the programs it depends on (i.e.
sander).
Hope that helps.
-Bill
On Mon, May 19, 2025 at 5:28 AM Mar Llorca Torres via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER Support Team,
>
> I hope this message finds you well.
>
> I am writing to ask for your help regarding an issue I’ve encountered with
> MMGBSA energy calculations. Specifically, everything in my calculation
> appears to work correctly *except for the van der Waals (VdW) energy
> terms*,
> which are giving unrealistic values.
>
> After trying various parameter changes in my own system without success, I
> decided to follow the official AMBER tutorial found here:
> https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.php
>
> I downloaded the provided tutorial files (ras-raf_top_mdcrd.tgz) and ran
> the MMGBSA calculation using the following simplified mmpbsa.in file
> (since
> I am only interested in the GB model):
>
> &general
> endframe=50, verbose=1,
> /
> &gb
> igb=2, saltcon=0.100,
> /
>
> Unfortunately, I obtained the *same VdW issue* even with the tutorial
> files. All other energy terms match the expected values, but the van der
> Waals term differs significantly.
>
> I am attaching a comparison between the results from the tutorial (white)
> and my calculation (black), showing that the only discrepancy lies in the
> VdW energies. I have also attached both FINAL_RESULTS.dat files for your
> reference.
> [image: image.png]
>
>
> Could you please help me understand what might be causing this issue, and
> how I could correctly compute the VdW contributions?
>
> Thank you very much in advance for your time and assistance.
>
> Best regards,
> *Mar Llorca*
>
> --
>
>
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--
Bill Miller III
Associate Professor of Biochemistry
A.T. Still University
417-549-0952
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Received on Mon May 19 2025 - 08:00:02 PDT
