Re: ValueError: math domain error

[Mario Sergio Valdes]

The standard deviation propagation does not work for so few frames. This is because the term |-2*std1*std2| > std1^2 + std2^2, which ends up making the term inside the root negative. Use more number of frames

El miércoles, 30 de marzo de 2022 a las 18:05:27 UTC-5, 20140003835 escribió:

Hi, 

can anyone help me with this, i got the following error upon running the software. Just before this, I was able to successfully run a system with the same molecules, atomtypes, and forcefield (OPLS).

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 2 frames were processed by cpptraj for use in calculation.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning PB calculations with /opt/amber/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Parsing results to output files...

  File "/home/hanah/.local/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 112, in gmxmmpbsa
    app.parse_output_files()
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 1049, in parse_output_files
    self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'],
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 789, in __init__
    self._delta()
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/amber_outputs.py", line 815, in _delta
    self[key] = temp.corr_sub(self.lig[key])
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/utils.py", line 89, in corr_sub
    comp_std = get_corrstd(self_std, other_std)
  File "/home/hanah/.local/lib/python3.8/site-packages/GMXMMPBSA/utils.py", line 133, in get_corrstd
    return sqrt(val1 ** 2 + val2 ** 2 - 2 * val1 * val2)
ValueError: math domain error
Exiting. All files have been retained.

hoping anyone could help me with this. thank you.

[20140003835]

it worked. thank you so much