can we use openbabel instead of meeko to prepare PDBQT files?

[RJ-Li]

we had trouble with meeko to prepare receptor pdbqt file:

mk_prepare_receptor.py -i 5tmn_protein.pdb -o 5tmn -p
mk_prepare_receptor.py: error: unrecognized arguments: -i 5tmn_protein.pdb -p

and we find it convenient to use openbabel:

$ obabel -ipdb 5tmn_protein.pdb -opdbqt -O 5tmn_protein.pdbqt
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is 5tmn_protein.pdb)

1 molecule converted

so is it correct to use obabel to prepare the pdbqt files? We didn't find that obabel approach recommended on your document website. https://autodock-vina.readthedocs.io/en/latest/docking_requirements.html#meeko

[rwxayheee]

Hello @RJ-Li
That might to be a version issue. Could you try to re-install the latest meeko=0.6.1?

mk_prepare_receptor.py -i 5tmn.pdb -o 5tmn -p 

worked for me with the raw 5tmn.pdb file from Protein Data Bank. See output:
5tmn.pdbqt.txt

I am responsible for the latest update on Vina documentation, but before that it didn't mention obabel for receptor preparation. Personally, I do not recommend obabel to prepare pdbqt file. Meeko uses a more sophisticated approach to perceive the macromolecule structure from PDB file by sanitizing the chemical structure. While Meeko is more stringent in its processing, it provides a feedback on any issues in the input file. You can at least use Meeko to pre-screen the receptor PDB file, and resort to Obabel only if you really need a quick workaround ^^