During extraction of the docking poses, in some cases, obabel seems to give error messages. The error results in the individal ligand docking.pdb files to be wrong, when opening in e.g. AutoDock or Chimera, and misses certain bonds between atoms.
Does somebody know how to fix these .pdb file either in batch or individually?
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is docking.out.pdbq
*** Open Babel Error in TetStereoToWedgeHash
Failed to set stereochemistry as unable to find an available bond