Obabel errors: unable to find bonds

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

The cause of this phenomenon is that pdbqt files are missing the exact connectivity information (since this is not relevant for docking with AutoDock Vina and similar). Vina only needs to know which bonds are rotatable.

Open Babel tries to guess the connectivity when converting to pdb (chemical sensing), but it doesn’t get it right all the times. Thus the docking poses are mainly useful to see where the atoms of the molecule are. However, if you want to see the actual molecule with the proper connectictivity, each pdbqt output and input file of VirtualFlow version of the REAL library, as well as the pdb output files, contains the SMILES string of the molecule.