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.

Jeslyn_Jaic · November 17, 2025, 4:23pm

Dear Jennifer

Thank you for your support and guidance so far. I reviewed the GitHub link you provided, but I am not sure how it applies in my situation since I am working within Galaxy rather than the command line, and I do not fully understand the code. After checking my ligand files again, I realised that I am using the salt forms of existing drugs, which may be causing the issue. Is there a way in Galaxy to ensure that salts are ignored so that only the active part of drug is used for docking?

Thank you

simonbray · November 18, 2025, 1:32pm

Hi @Jeslyn_Jaic

You could try this tool: Galaxy

Or search “remove counterions” if you’re not on usegalaxy.eu

Hope it helps

Simon

Jeslyn_Jaic · November 18, 2025, 7:05pm

Dear Simon,

Thank for the suggestion, I just tried the tool but its showing tool error. It also didn’t give an error message so Im not really sure what happened. I have attached the history as well.

https://usegalaxy.org/u/jeslyn.jaic/h/unnamed-history

jennaj · November 18, 2025, 7:33pm

HI @Jeslyn_Jaic

The job runs on your files at UseGalaxy.eu. Please try there instead while we sort out the tool dependency/resource issues at UseGalaxy.org.

You don’t need to start over! FAQ: How to move files between Galaxy servers by URL

Glad you are getting closer to a solution!

jennaj · November 18, 2025, 7:52pm

Update: I see the problem. There are two versions of the tool – and one is older and should be avoided.

Tool panel

Use the first one, named: Remove counterions and fragments from a library of compounds(Galaxy Version 3.1.1+galaxy2)

We keep both because we keep everything (for reproducibility reasons) however we should probably hide the older version in the searches. I’ll work with our administrators to do this.

Tool panel -- hide ctb_remIons/1.0. (replaced by openbabel_remIons/3.1.1+galaxy2) · Issue #1198 · galaxyproject/usegalaxy-tools · GitHub

So – you can continue to work at UseGalaxy.org for this!

Jeslyn_Jaic · November 21, 2025, 12:16pm

Thank you for the clarification regarding the counterions tool. It worked however, when I run the resulting file into Vina, I still encounter an error. I also tried using the ‘Prepare Ligands for Docking’ tool, which generates individual PDBQT files, but these also produce errors when I attempt to run the file with the Vina docking tool. I also looked at the training module which used a ‘compound conversion’ tool, however the output file also results in errors when I use it for the vina docking tool

Is there any other tool that can be used to prepare the ligands file before running it on Vina docking tool ?

jennaj · November 21, 2025, 7:05pm

Hi @Jeslyn_Jaic

Let’s try to solve the error you had with this part. Would you like to share the history again? Or is this in your prior history? I want to make sure we are both looking at the same thing. Please make sure that all steps are included – from the original PDB through to the preparation of the protein and the ligand(s). I’d like to trace back through to see if we can notice where the problem is coming up e.g. data content versus some tools problem (bug or parameter we can tune up!).

Then, as a reference, I am working through this tutorial directly! I am up through the Vina Docking step (so far). The idea is to create an example of all tutorial steps, but also to flush out issues with these tools at the UseGalaxy.org server. I was able to dock 13 ligands in the batch run!

I only ran into one problem so far and it was corrected by selecting different output files (I’ll be reporting this). This is an example of the type of parameter tunings that can get around technical errors with these very complicated scientific tools!

Finally, for this part:

These tools will work the same in Galaxy as they do when used on the command line (they are the same underlying tools). The only difference is that the options are presented on a web form. This means if the underlying tool cannot process a particular data file, then that same processing won’t be possible in Galaxy.

This also means that reviewing known situations that are reported in other places like Github can be useful for us as we work through the problems you are running into when using the same tool in Galaxy. In particular, the error messages can be searched to locate these discussions. Asking an AI assistant is also possible since they are surprisingly good at parsing technical user manuals (but double check the advice of course!).

So, if you would like to share back what you have, let’s try to sort out what is happening: data content, versus parameter, versus (possibly) buggy behavior with the Galaxy wrapped version of the tool. This is the purpose of this forum and I’d like to get this working for you!

Jeslyn_Jaic · November 23, 2025, 7:20am

Thank you for your guidance and support so far and yes its all in the same history.

The receptor file is 6CDY which I removed the ligand on chimera and then used the ‘prepare receptor’ tool on galaxy (This is job number 21)

The ligand file was taken from the ZINC database and has 1040 molecules and as you had mentioned that it might be a metadata problem I divided the file into 4 files of 260 molecules each using biovia. I then used the ‘prepare ligands for docking’ tool for one of the ligand files and then this gave 260 individual PDBQT files (this is job number 8807)

I then put these 260 PDBQT files for the ligands into ‘Vina’ tool so it docking of each ligand and many of them resulted in errors.

jennaj · November 24, 2025, 8:25pm

Thanks @Jeslyn_Jaic for letting me know that the original history is where you are working! This one is getting near 10k datasets .. which is about the limit for a web browser to keep track of the display items. I would suggest using Copy Datasets or Copy History soon (at least leaving the deleted items behind).

For these, you have seen the error, correct?

The error message from the tool is reporting that the input wasn’t formatted correctly. Example from one of them:

Then the input had a message. Are you sure this is a potential ligand?

Moving on to more recent jobs in that history..

From what I can see, it seems like you saw the error for the latest batch job about finding an unexpected “ROOT” term in a pdbqt prepared ligand input (where dataset 6631 was the original baseline). And, that you interpreted this error correctly: pdbqt format is for a single ligand (where ROOT would be unexpected, hence the error) and to use sdf format when there are multiple ligands. Since you have multiple ligands, converting is the next step. And, I can see that converting to sdf format is failing for running out of memory resources!

I think this is an actual tool memory resource issue, and not a problem with the content, especially since runs through the conuterions/fragment tool didn’t modify the content. I’ve put in a request to have the memory allocation reviewed, but this will not be immediate, and it may mean the downstream tools like Vina Docker itself will also need more resources!

Request: increase memory allocation for openbabel_compound_convert/3.1.1+galaxy1 · Issue #1210 · galaxyproject/usegalaxy-tools · GitHub

What to do:

Use sdf format

Split up your ligands into even smaller chunks since 260 is still too many all at once. How many files shouldn’t really matter if you place these inside of a flat list collection. 100 files with ~10 ligands each would have as many manual processing steps as one file with 1000.

Then, work with one of those subsets to tune all of the steps until it is working, extract a workflow, then run that workflow on the whole batch?

Or, use pdbqt format

One file per ligand, also in a collection. But you’ll need to correct the format for “prepared” correctly. The tutorial has examples for this – notice the bonus exercise in particular. I included this in my history from last week. It goes through how to query for exploratory reasons against public databases but also how to filter those lists, then how to reformat. I think this will help you, too, when using the other software to produce potential ligands. Do these need to be filtered more?

I would also suggest a subset for this method: maybe 10 files. Get this working, then run on the whole thing.

Hope this helps! I think you are getting closer.

Jeslyn_Jaic · November 24, 2025, 10:37pm

I used a ligand file containing 10 molecules and converted it using the ‘compound conversion’ tool, which appeared to function correctly as the job was highlighted in green. However, I am not sure why an error message is being generated.

I then inputted this file into vina and I did get results but the but they are all highlighted in red and the same error message is showing.

I am using a history called ‘New history’ which is https://usegalaxy.org/u/jeslyn.jaic/h/new-history

Thank you for taking the time to look into this.

jennaj · November 25, 2025, 12:58am

So this type of multi-ligand dataset must be given to the docking tool in sdf format, instead of pdfqt.This is what I meant with this comment:

And this is the part of a tool form with some of these details explained (the full tool docs have more).

Your current error is about a multi-ligand showing up in the unexpected file type. Please try the other format instead to see what happens!

Jeslyn_Jaic · November 25, 2025, 8:04am

I not sure what you mean cause the ligand file that I inputted into vina is in the SDF format. I have attached a screenshot for your reference as well.

jennaj · November 25, 2025, 6:11pm

Hi @Jeslyn_Jaic Thanks for clarifying. I had to moderate some of your posts so the data was out of order! I’m reviewing the new job now – the history is smaller and clearer which is great! More soon.

jennaj · November 25, 2025, 7:08pm

Hello – these are my observations.

The failure when using the sdf file is due to duplicated entries with the same Name.

How did I find that?

I converted the original mol2 ligand file (with multiple entries) into split pdfqt files with one molecule in each to help isolate the jobs per molecule. This is sort of like detective work in an attempt to see exactly where the problem is.

History – I tagged the datasets and hid the other errors.

Then, I ran the job on the collection of pdfqt ligands as a batch. Click into collection 45 to see which were successful (one result each) and which failed (no output). Three failed in total, and one was molecule9. So, I reran the job with just the molecule9 (rerun icon for one of the jobs, then dragged over the original input dataset out of the collection on to the form).

This also failed! So, I know this wasn’t a cluster problem but a data problem. From there, I examined the content of that failure datasets verses a molecule that was successful (molecule8 was my choice, but you can look at others too!). From there, I could see that all of the successful molecules had one entry, and the failures each had unexpected content (6, 9, and 10).

molecule9

The tool error about ROOT is the tool detecting multiple molecules with the same Name, which is unexpected in either sdf or pdfqt format, so I would focus on resolving this in the original file. Then review the other entries with format issues: molecule6 and molecule10 to see if you can inspect and correct. The tool might produce a different or more informative message with those if were also run individually.

This is my copy of your history if you would to look at it. → https://usegalaxy.org/u/jen-galaxyproject/h/copy-of-new-history-https-help-galaxyproject-org-t-error-when-running-molecular-docking-16409-15

I just started up the individual runs!

molecule10 – duplicated Name, same as molecule9
molecule6 – still executing. I don’t see a duplicated Name but maybe you can notice what the problem is in the entry (inspect with eye icon) or review the log once this completes. My guess is a tag problem. We can also review together. This one is now successful! The original error may have just been transient. We run thousands of jobs every hour – a tiny fraction fail by chance.

So, given these results – resolving the Name duplicates is actually what to focus on.

Hope this helps! Great work on this!

Jeslyn_Jaic · November 25, 2025, 9:25pm

I visualized the MOL2 file for ligand 9 and noticed that the presence of a salt group appeared to cause an error during conversion to the PDBQT format. After removing the salt using BIOVIA and reconverting the ligand 9.mol2 file, the resulting PDBQT file no longer contained duplicate entries with the same ‘Name’.

To avoid this issue, I applied the ‘Remove Counterions’ tool prior to performing the ‘Compound Conversion’ step. I then inputted the resulting set of 10 molecules through Vina, and it worked this time. (This is job number 42)

Since I had previously tested this method on a file containing 260 molecules, it may have failed due to the large file size. I will therefore divide the remaining molecules into sets of ten and see whether the method works consistently across the smaller batches.

Thank you for your support and for pointing me in the right direction.