error on running gmx_mmpbsa

[Justice Mallen]

Hi all,

i am having this error when i run gmx_mmpbsa, i have attached the log file as well.

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /tank/data/LS/saha6/conda/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##################################################################################################| 301/301 [elapsed: 05:59 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##################################################################################################| 301/301 [elapsed: 05:47 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##################################################################################################| 301/301 [elapsed: 00:01 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 "/tank/data/LS/saha6/conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/uwm/jjmallen/.local/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/home/uwm/jjmallen/.local/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/uwm/jjmallen/.local/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/home/uwm/jjmallen/.local/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/home/uwm/jjmallen/.local/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 630, in _get_energies
    self['BOND'][self.frame_idx] = conv_float(words[2])
  File "/home/uwm/jjmallen/.local/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/uwm/jjmallen/.local/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.
Exiting. All files have been retained.

[Mario Ernesto]

Please, check the link provided...

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions

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