Some energy terms are undefined.

[Vasyl Hurmach]

Hi all,

Could you please help me? How can I fix that?

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /home/work/INSTALED/pymol/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 11/11 [elapsed: 02:15 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 11/11 [elapsed: 02:28 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 11/11 [elapsed: 00:02 remaining: 00:00]
[INFO   ] Parsing results to output files...

[ERROR  ] MMPBSA_Error

Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1211, in parse_output_files
    self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 740, in _get_energies
    self['BOND'][self.frame_idx] = conv_float(words[2])
  File "/home/work/INSTALED/pymol/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 603, in conv_float
    GMXMMPBSA_ERROR('Some energy terms are undefined. Please, check the input structure and trajectory. Check this '
  File "/home/work/INSTALED/pymol/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.')
MMPBSA_Error:

Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

[Mario Sergio Valdes]

Please, follow the link (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions)