Error running gmx_MMPBSA as "failed when querying step5_1.tpr"

[Nitesh Mani]

Dear Mario,

I am running binding energy calculations of a protein-peptide system.The MD simulation system was prepared using CHARMM-GUI and it is showing the error:

[ERROR  ] MMPBSA_Error /usr/local/gromacs/bin/gmx editconf failed when querying step5_1.tpr.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/ablab/anaconda3/envs/MMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ablab/anaconda3/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 95, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ablab/anaconda3/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 576, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ablab/anaconda3/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 115, in buildTopology
    self.gmx2pdb()
  File "/home/ablab/anaconda3/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 166, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.editconf), self.FILES.complex_tpr))
  File "/home/ablab/anaconda3/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /usr/local/gromacs/bin/gmx editconf failed when querying step5_1.tpr. Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Logfile is attached for your reference

Kindly help in this regard.

Best Regards,

Nitesh

[Mario Ernesto]

Hi and welcome! In the command line, you specify the smae group as receptor and ligand groups '-cg 0 0' and that's why gmx_MMPBSA fails on identify successfully the receptor and the ligand groups... Make sure to create a separated group for the receptor and one for the ligand in the index file and then use those in the command line...

hope this helps!

Mario E

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