I'm looking to convert a PDB to PDBQT file but I am getting the failed to kekulize aromatic bonds error, which I suspect is leading to an "unknown or inappropriate tag" error in Vina.
Originally, the command I used was obabel "AlphaFold Generated.pdb" -O "AlphaFold Generated1.pdbqt" but it gave me the warning Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is AlphaFold Generated.pdb). Taking suggestions from the internet I added obabel "AlphaFold Generated.pdb" -O "AlphaFold Generated1.pdbqt" -h but I am still seeing the same error displayed. Not sure if this is relevant, but the PDB file was predictively generated on AlphaFold. Thank you , Ilinca
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