I would suggest checking the MMPBSA.py mdout files. If the calculations ends abruptly with a prmtop failure, that’s probably where the error message is. You should also search the mdout files for ***** that would be listed any place the energies are outside the bounds of the space (such as high energies resulting from overlapping atoms).
Hope that helps.
-Bill
> On Jan 15, 2024, at 7:01 AM, VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org> wrote:
>
> Hi everyone
>
> I'm running a MMGBSA calculation of a complex-ligand structure, and it could happen two things: one is a failure in the calculation due to a prmtop file, but I have examinated the temporary files and there is nothing in the files, just the calculation stops. The second, when the calculation doesn't fail, I've got bizarre values of the VanderWaals forces. This could happen because the structure that we are considering (a ribosome) is too big and there are many overlappings? Because I don't know where the errors are now in this calculation
>
> Thanks in advance
> Verónica
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Received on Mon Jan 15 2024 - 07:00:02 PST
