ValueError: could not convert string to float: '*************'

[Sanjay Kumar]

After job completion this error throw by program

please help me

CHAMBER prmtops found. Forcing use of sander
Preparing trajectories for simulation...
19996 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/ravishankar/.conda/envs/AmberTools21/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...
  File "/usr/local/bin/gmx_MMPBSA", line 11, in <module>
    sys.exit(gmxmmpbsa())
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/app.py", line 121, in gmxmmpbsa
    app.parse_output_files()
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/main.py", line 966, in parse_output_files
    self.using_chamber)}
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/amber_outputs.py", line 664, in __init__
    AmberOutput._read(self)
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/amber_outputs.py", line 341, in _read
    self._get_energies(output_file)
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/amber_outputs.py", line 676, in _get_energies
    self.data['BOND'].append(float(words[2]))
ValueError: could not convert string to float: '*************'
Exiting. All files have been retained.

[marioe911116]

Hello there! 

please, check this section (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/Q%26A/calculations/#possible-solutions) in the documentation... 

Also, feel free to share more details about your system, that way we can give you better advice...

cheers!

Mario E.

[Sanjay Kumar]

Thanks mario,

got the solution from your given section, yes problem in my topol.top file that I have fixed it.

A large number of frames takes more time, 20000 frames takes 3 days in my 32 processors so I reduced it.

[Mario Sergio Valdes]

The calculation time depends on the solvent model you are using for the calculation (PB or GB) and the parameters you configure for it. For the article (https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645) we made the GB calculation for 200,000 frames in 60 cpu, for the system and the mutant and it took about 3 days. PB takes about 5x more time (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/command-line/#running-gmx_mmpbsa).

We hope you don't have a problem with gmx_MMPBSA or gmx_MMPBSA_ana. In our case, they worked as expected.

Mario S.