Re: [AMBER] Error in MMPBSA

From: Bill Miller III via AMBER <>
Date: Wed, 15 Nov 2023 06:28:50 -0600

I don’t believe the actually helpful error message is here. Check the end of the complex mdout file(s). I’m guessing there is an error message in there that will reveal the actual problem.


> On Nov 15, 2023, at 6:15 AM, VERONICA MARTIN HERNANDEZ via AMBER <> wrote:
> Hi everyone and sorry for asking too much. I performed a MD and I want to calculate MMGBSA, but I've got the next error:
> Loading and checking parameter files for compatibility...
> cpptraj found! Using /home/soft/Amber22/amber22/bin/cpptraj
> mmpbsa_py_energy found! Using /home/soft/Amber22/amber22/bin/mmpbsa_py_energy
> Preparing trajectories for simulation...
> 2 frames were processed by cpptraj for use in calculation.
> Running calculations on normal system...
> Beginning GB calculations with /home/soft/Amber22/amber22/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/home/soft/Amber22/amber22/bin/", line 100, in <module>
> app.run_mmpbsa()
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/", line 224, in run_mmpbsa
>, self.stdout)
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/", line 519, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /home/soft/Amber22/amber22/bin/cpptraj failed with prmtop structure-dry.prmtop!
> Fatal Error!
> All files have been retained for your error investigation:
> You should begin by examining the output files of the first failed calculation.
> Consult the "Temporary Files" subsection of the chapter in the
> manual for file naming conventions.
> Apparently is the prmtop of the structure-dry. But I have tried to generate the file with tleap and the structure looks well . In addition I have tried generate it with ante-MMPBSA and everything I have tried, has not worked
> Could anyone help me with this issue?
> Thanks in advance
> Verónica
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Received on Wed Nov 15 2023 - 04:30:03 PST
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