I don’t believe the actually helpful error message is here. Check the end of the MMPBSA.py-generated complex mdout file(s). I’m guessing there is an error message in there that will reveal the actual problem.
-Bill
> On Nov 15, 2023, at 6:15 AM, VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org> 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/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/home/soft/Amber22/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", 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 MMPBSA.py 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
