Hi Johnny,
I don’t see anything obviously wrong with your python script itself that would cause the crash, but as mentioned below you may want to try debugging each step. There could also be an issue with your input files. For debugging, I would suggest creating a simplified model that reproduces the error to help narrow down what specifically is causing the error. Maybe you can shorten the structure to a point where it works and then find which part that causes the crash when it's added to the structure.
If you can share the input files or a smaller set that reproduces the error, then someone may be able to help find the problem, but it's difficult to tell just by looking at the python script if anything is missing.
Jason
________________________________
From: David A Case via AMBER <amber.ambermd.org<mailto:amber.ambermd.org?Subject=Re%3A%20%5BAMBER%5D%20Problems%20with%20MMPB%2FMMGBSA>>
Date: Sat, 2 Aug 2025 14:39:14 -0600
On Sun, Jul 27, 2025, Johnny Su via AMBER wrote:
>
> I've tried multiple methods but I keep ending up with all
>Frames corrupting at the origin and am incapable of fixing it despite weeks
>of trial/error. Hope someone could assist in this endeavor.
The python script you attached is not very helpful. Many things can go awry
with MMPBSA, and in debugging it is important to try to work step-by-step to
find the first error.
In this case, it is hard to understand what you mean by "all Frames
corrupting at the origin". Can you try to work through the steps as much as
possible "by hand", and provide information about the actual error message
that pops up first?
...thx...dac
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Received on Wed Aug 06 2025 - 18:00:03 PDT
