Error when running molecular docking

Jeslyn_Jaic · October 20, 2025, 11:09am

I’m encountering an error while running a molecular docking simulation. I’ve attached the full error message below. Could someone please help me understand what’s causing the issue and how to resolve it?

Thank you for your time and support

Tool ID -toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0

*** Open Babel Warning  in ReadUnimplementedBlock
  COLLECTION blocks are not currently implemented and their contents are ignored.
1123 molecules converted
1123 files output. The first is ligand1.pdbqt


PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Atom type B is not a valid AutoDock type (atom types are case-sensitive).
 > ATOM      1  B   UNL     1      -1.214  -2.726   0.000  0.00  0.00    +0.000 B 



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT




==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)


*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Atom type B is not a valid AutoDock type (atom types are case-sensitive).
 > ATOM     11  B   UNL     1       0.750  -9.093   0.000  0.00  0.00    +0.000 B 

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

=================
..
s in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond


PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond


PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Atom type Au is not a valid AutoDock type (atom types are case-sensitive).
 > ATOM      9 AU   UNL     1       3.750  -1.299   0.000  0.00  0.00    +0.000 Au



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is =)



PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond
==============================
*** Open Babel Error  in TetStereoToWedgeHash
  Failed to set stereochemistry as unable to find an available bond


PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT

jennaj · October 21, 2025, 12:27am

Welcome @Jeslyn_Jaic

I just replied to another question about an error with this same tool. Was this also yours? Empty Output folder - Vina Docking

If not, maybe the content helps. Meanwhile, I am generating an example history from our tutorial and will post that back next. I’ll be using the data and workflow from here. My test will confirm that the tools are working as expected.

Hands-on: Protein-ligand docking / Protein-ligand docking / Computational chemistry

You could also try to see how the processing flows through the tool but maybe more importantly for your use case, examining the content of the files seems more important.

Why? You messages are about the content of your ligand inputs.

What happens if you split up the multi-ligand SDF first, then run the collection of PDBQT files through this tool? Something like this:

More soon as a process the tutorial. Once you have results from the splitting, you can also post back. Sharing the history is an easier way to offer feedback and involves just a single link. You can unshare after we are done. → How to get faster help with your question

Let’s start there, thanks!

Jeslyn_Jaic · October 30, 2025, 12:05pm

I tried splitting the file into two parts using BIOVIA and then reran the process, but the same error still occurs (each individual file containing 520 molecules each).

Previously, I also attempted converting the file into individual PDBQT files. While some of those jobs completed successfully, many produced errors, and managing such a large number of separate files wouldn’t be practical for future analysis or result comparison.

This is the url of the history - https://usegalaxy.org/u/jeslyn.jaic/h/unnamed-history

I’d really appreciate any suggestions or advice on what to try next.

jennaj · October 30, 2025, 11:14pm

Thanks for sharing the history! Very helpful.

Now, big picture, I think it worked this time! Models seem intact. You can click on the eye icon for any of those errors at the top of your history and explore them in the viewer, but also see the raw files.

There might be a metadata problem, I’m checking and feedback might be tomorrow. If this is why the dataset are still “red”, that can be cleared, and the results you have now would be useable. But – I’m optimistic, so let’s also move forward on more.

Since I think we will need some help from a proteomics person to completely sort this out, I’ve crossposted over to a chat that should attract some Galaxy people who work in this domain, including the scientist who wrote most the tool wrapper you are using. They will reply back here. Please be sure to leave your history shared so they can see the technical details!

Then, let’s also ask some administrators who understand the tool. Hi @bjoern.gruening do you have time to take a quick look? Thanks!

More soon!

jennaj · October 31, 2025, 5:28pm

Hi @Jeslyn_Jaic

I have some more information from some Galaxy scientists working in a related domain!

There is a specific way to do the formatting according to the researchers here, and they also include more details. The errors they were getting from using this tool directly look very much like your error.

github.com/openbabel/openbabel

Parsing error issue with obabel generated pdbqt files in vina

opened 01:19PM - 16 Jan 24 UTC

closed 03:17PM - 16 Jan 24 UTC

AlexisGGk

Ive been converting pdb structures for use in autodock vina using obabel. I …get this error in autodock vina Parse error on line 2444 in file "receptor_4.pdbqt": Unknown or inappropriate tag when I check this line it says ROOT. Out of curiosity I tried just deleting that line and it immediately flags up the following lines instead. The format of the file appears correct and when I used obabel to convert small molecules from the smiles the system has no issue with it this is the line I used for the conversion obabel receptor_3.pdb -O receptor_4.pdbqt -h -gen3D I have tried lots of variations and using different structures etc. but always the same issue. Ive also tried using the online version of obabel and when I select add hydrogens and generate 3D co ordinates it simply gives a blank output. When I don't include this it works but because there aren't 3D co ordinates it can't be used attached here is the output. I am sure it's some silly mistake but I can't see it [receptor_5.txt](https://github.com/openbabel/openbabel/files/13950454/receptor_5.txt)

Notice the part about the receptor needing to “be rigid” and the flags to use with that other tool but more importantly, the content that is added to the PDBQT file, since is required by VINA. The Prepare Receptor tool in Galaxy should be doing this when generating a PDBQT output for use with Vina.

I’m also going to try to look but this outside my domains of expertise, and I wanted to share this feedback since you may notice what is wrong quicker, and maybe there is something more needed in your upstream PDB input instead.

More soon and let us know what you also find! I’d like to get this solved for you.