Parsing outputfiles Error

[akr rathee]

Hey Mario :)

I hope that you are doing well.

Sorry for the new question, a problem bubbled up again.

 mpirun -np 48 gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci complex.ndx -cg 1 13 -ct md_0_10.xtc -lm unk_bcc_gaff2.mol2 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  mpirun -np 48 gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci complex.ndx -cg 1 13 -ct md_0_10.xtc -lm unk_bcc_gaff2.mol2 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/user/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/user/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/user/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/user/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/user/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] Generating ligand parameters from unk_bcc_gaff2.mol2 file...
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected Amber/OPLS force field topology format...
[WARNING] 6 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

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


[INFO   ] 250 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 48 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/user/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 250/250 [elapsed: 00:33 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 250/250 [elapsed: 00:31 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 250/250 [elapsed: 00:01 remaining: 00:00]
[INFO   ] Beginning PB calculations with /home/user/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 250/250 [elapsed: 09:06 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 250/250 [elapsed: 08:48 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 250/250 [elapsed: 00:07 remaining: 00:00]
[INFO   ] Parsing results to output files...

  File "/home/user/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/user/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
    app.parse_output_files()
  File "/home/user/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1053, in parse_output_files
    self.calc_types.normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
  File "/home/user/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 108, in parse_from_file
    AmberOutput._read(self)
  File "/home/user/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 197, in _read
    self._get_energies(output_file)
  File "/home/user/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 610, in _get_energies
    self['BOND'][self.frame_idx] = float(words[2])
ValueError: could not convert string to float: '*************'
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Please let me know if you need some files... i will share to you 

Thank you so much in advance, and for caring so much for the support :)

Best regards

[Mario Ernesto]

This is a comoon error when the trajectories are not treated properly before using gmx_MMPBSA... Please, check 

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/gmx_MMPBSA_running/

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