The actual error message isn’t in this log file. The problem occurred during the energy calculation step. So, check the end of any mdout files that were generated by MMPBSA.py instead. There should be a fatal error message printed there.
-Bill
> On Jul 19, 2023, at 3:47 PM, Ramachandran, Balajee via AMBER <amber.ambermd.org> wrote:
>
> Dear Friends
>
> I have performed the simulation for the protein-ligand complex. I would like to perform the MMPBSA analysis (since it was the first run, I started with first 10 frames). I am getting the following error.
>
> Input:
>
> Input file for running PB and GB
> &general
> endframe=10, verbose=1,
> receptor_mask=':1-1082',
> ligand_mask=':1085',
> keep_files=2, interval=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> mmpbsa_py_energy found! Using /software/pkg/amber/22/install/bin/mmpbsa_py_energy
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with software/pkg/amber/22/install/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "software/pkg/amber/22/install/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File "software/pkg/amber/22/install/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/software/pkg/amber/22/install/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/software/pkg/amber/22/install/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 475, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /software/pkg/amber/22/install/bin/cpptraj failed with prmtop a1.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.
>
> Please suggest me how to recover from this error.
>
> Thanks
>
> regards
>
> Balajee
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Received on Wed Jul 19 2023 - 14:00:02 PDT
