Hi Veronica,
The actual error should be described at the very bottom of one of the
output files that were retained. You can find them in the same directory
where you ran the program from (unless you pointed them elsewhere).
Check it and see if it makes sense.
Hooenit helps
Pedro
On Wed, Nov 15, 2023, 13:11 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 - 05:00:02 PST
