CalcError:

[Sridhar Kulkarni]

Hello,

I have tried to do gmx_MMPBSA for the groups as said and continued with the solution you provided to other member of group about this error. This error is appearing even apter centring and fitting the trajectory. The GB calculations are going through well. But PB calculations has problem. I have done the gmx_MMPBSA befor and the error was not shown then. Please help me overcome this error.

Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 50/50 [elapsed: 00:30 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 50/50 [elapsed: 00:32 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 50/50 [elapsed: 00:01 remaining: 00:00]
[INFO   ] Beginning PB calculations with /home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/50 [elapsed: 00:00 remaining: ?][ERROR  ] CalcError

/home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/home/bif-sssihl-12/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
CalcError:

/home/bif-sssihl-12/miniconda3/envs/AmberTools23/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 6.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6

[Mario E. Valdes-Tresanco]

Please, sends us the *.mdout files

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[Sridhar Kulkarni]

https://drive.google.com/drive/folders/1fV-JI-b3bRh8zUd6zOcN78AnF77RyGZd?usp=sharing

Here are the .mdout files. Thank you for you immediate reply.

[Mario E. Valdes-Tresanco]

I don't see anything wrong... please run the calculation with one processor (no parallelization) and see if it ends up in error...if so, send the mdout file

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[Sridhar Kulkarni]

That worked. Running in only one CPU the calculation went on smooth. Thank you for your immediate reply and solving the problem.

[gmx_MMPBSA]

Please check this link (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/gmx_MMPBSA_running/#running-gmx_mmpbsa). Note that PB and NMODE calculations require a lot of RAM, depending on the system size.