Error during Parsing results to output files

[douaki ali]

Good morning,

I am getting the following error.  Could you please help me with it!

[INFO   ] Parsing results to output files...

  File "/home/ali/miniconda3/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1048, in parse_output_files
    self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 653, in _get_energies
    self['BOND'][self.frame_idx] = float(words[2])
ValueError: could not convert string to float: '*************'

Exiting. All files have been retained.

[Mario Ernesto]

Please, check this section in the docs

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

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[douaki ali]

Hi Mario,

Thank you for the reply.

Is there a way to extract the results manuly form the already created files instead of reporfomring the calculations from the scratch?`.

[Mario Ernesto]

Unfortunately, you will have to perform the MMPBSA calculation from scratch using the fitted trajectory 

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/5bd345af-4424-4ba5-ad2d-4ef76755a923n%40googlegroups.com.

[douaki ali]

Hi Marioe,

Thank you for the reply. after fixing the structure consistenc, now the error is fixed.

Have a nice day.

[marioe911116]

great!