From: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
Date: Wed, 15 Nov 2023 12:10:27 +0000

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>
  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

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Received on Wed Nov 15 2023 - 04:30:02 PST
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