parmchk2 failed when querying LIG.mol2

[Kayode Raheem]

Hi

I am trying to perform QM/MMGBSA calculation but having this error with parmchk2 failed to query the LIG.mol2

Here is the error getting:

 mpirun -np 12 gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index.ndx -cg 1 13 -ct MD_center.xtc -lm LIG.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO   ] Starting gmx_MMPBSA v1.6.2
[INFO   ] Command-line
  mpirun -np 12 gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index.ndx -cg 1 13 -ct MD_center.xtc -lm LIG.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Writing qmmm_region.pdb PDB file of the selected QM region...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/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 Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] Generating ligand parameters from LIG.mol2 file...
[ERROR  ] MMPBSA_Error

/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/parmchk2 failed when querying LIG.mol2

Check the gmx_MMPBSA.log file to report the problem.
tets
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 682, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
    self.gmx2pdb()
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 326, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (parmchk2, self.FILES.ligand_mol2))
  File "/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:

/home/kayode/Documents/Kayode_Lab/Tools/home/kayode/Documents/Kayode_Lab/Tools/mamba/envs/gmxMMPBSA/bin/parmchk2 failed when querying LIG.mol2

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

[gmx_MMPBSA]

Please, use the -cp topol.top flag and it should be ok