Error while running gmx_MMPBSA (Error: too many values to unpack)

[Gitanjali Tandon]

Hi

I have installed gmx_MMPBSA via conda environment.

After installing, when I activated the gmx_MMPBSA environment, it gave the warnings:

No ICDs were found.

This was rectified by using the following command:

conda install -c conda-forge ocl-icd-system

Finally I tried to run gmx_MMPBSA :

  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_100.tpr -ci index.ndx -cg 1 13 -ct md_0_100_fit.xtc -cp topol.top

It is showing the following error:

File "/home/gitanjali/.conda/envs/MMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 478, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/gitanjali/.conda/envs/MMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 357, in read
    name, num = line.split()
ValueError: too many values to unpack (expected 2)
Exiting. All files have been retained.

For reference I have also attached the log file.

Kindly suggest what to do.

[marioe911116]

This is probably an error in the topology... could you please send the topology file?

[Gitanjali Tandon]

THanks a lot for the reply..

Sure.. Please find the attached file..

[Mario Sergio Valdes]

Check line 85920 (1HET            1SOL             23640).

It should be:

1HET            1

SOL             23640

[Gitanjali Tandon]

Yes i corrected and it worked..

Thank you so much for your kind assistance