gmx_MMPBSA does not support water/ions molecules in any structure

[organic chemistry]

Hello Sir

I am getting the following error while running gmx_MMPBSA v1.6.3

gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ct md_dipeptideonly_monomer_center.xtc -ci index.ndx -cg 18 19 -cp protein.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/guju/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/guju/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/guju/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/guju/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/guju/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 a_1-172_a_173-344 (18_19) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[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 a_1-172 (18) 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 a_173-344 (19) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[ERROR  ] MMPBSA_Error

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/guju/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
                                                                          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 122, in buildTopology
    self.gmx2pdb()
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 519, in gmx2pdb
    self.check4water()
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 541, in check4water
    GMXMMPBSA_ERROR(f'gmx_MMPBSA does not support water/ions molecules in any structure, but we found'
  File "/home/guju/anaconda3/envs/gmxMMPBSA/lib/python3.11/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:

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

How to solve this problem?

Regards

[marioe911116]

could you please share the files you are using?

[organic chemistry]

Dear Sir

Sorry for the late reply. Actually it was an indexing error on our part which was causing the problem. It has been sorted out now. Thank you for your support.

Best regards

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