error while running gmx_MMPBSA

[Himanshi Gupta]

Hello,

I have installed gmx_MMPBSA and now trying to run this on protein-ligand system.

I used the command:

$ gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -lm unk.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

and I received the following error:

File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 293, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (parmchk2, self.FILES.ligand_mol2))
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/gbu/miniconda3/envs/gmxMMPBSA/bin/parmchk2 failed when querying unk.mol2
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Can you please help me out?

 Thank you so much!

[Sarthak Trivedi SVNIT]

Hi,

If you're system is prepared with CHARMM force field or not. I guess add flag -cp topol.top file instead of unl.mol2 file (replace -lm unl.mol2 with -cp topol.top) then let us know. That would work probably. But still I would like to request sir to verify my opinion.

Regards,

Sarthak.

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[marioe911116]

That's correct... you can use the -cp topol.top flag for any system and it should run smoothly

best!

[Himanshi Gupta]

Hi,

All my topologies have been prepared with GROMOS force field.

I tried the run replacing -lm unk.mol2 with -cp topol.top and I encountered further issue.

$ gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

File "/home/gbu/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/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/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/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/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 765, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 314, in read
    bond, bond_type = self._parse_bonds(line, bond_types, molecule.atoms)
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 511, in _parse_bonds
    bond = Bond(atoms[i], atoms[j])
  File "/home/gbu/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/topologyobjects.py", line 1718, in __init__
    raise MoleculeError('Cannot bond two virtual sites/extra points together')
MoleculeError: Cannot bond two virtual sites/extra points together

Exiting. All files have been retained.

Thank you!

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Himanshi Gupta

Research Scholar

Gautam Buddha University

Greater Noida - 201312

[Mario Sergio Valdes]

Unfortunately, GROMOS is not supported yet. We are working to implement other engines to compute PB with GROMOS, but it will take a while

[Himanshi Gupta]

Okay, Thank you!

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