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Cross-posted on Chemistry.SE.

I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools directory. The script converts pdb to pdbqt.

Usage

prepare_receptor4.py -r input.pdb -o output.pdbqt

input.pdb is the input pdb file, output.pdbqt is the output pdbqt file

I got the errors with 7RTT.pdb and 7WDA.pdb input files.

What are these errors and how can I resolve them? Any help will be highly appreciated.

Traceback (most recent call last):
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 204, in <module>
    dict=dictionary)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 558, in __init__
    version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 141, in __init__
    self.addCharges(mol, charges_to_add)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 227, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/MolKit/chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 143, in assignHybridization
    self.check_for_amides()
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 511, in check_for_amides
    if conn.babel_type=="Cac" or conn.babel_type=="Sox" or \
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/MolKit/molecule.py", line 409, in __getattr__
    raise AttributeError('member %s not found'%member)
AttributeError: member babel_type not found

and

Traceback (most recent call last):
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 204, in <module>
    dict=dictionary)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 558, in __init__
    version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 141, in __init__
    self.addCharges(mol, charges_to_add)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 227, in addCharges
    chargeCalculator.addCharges(mol.allAtoms)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/MolKit/chargeCalculator.py", line 80, in addCharges
    babel.assignHybridization(atoms)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 127, in assignHybridization
    a.babel_atomic_number = self.get_atomic_number(a.babel_type)
  File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 103, in get_atomic_number
    (name,_name) )
ValueError: Could not find atomic number for A A
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    $\begingroup$ I'll copy my comment from Chem.SE: It might help if you were a bit clearer about what you've tried doing. My guess, given the warning about macOS Catalina (released in 2019) is that it's not well-maintained anymore and may not parse modern PDB files. There is a specific support mailing list. $\endgroup$
    – Geoff Hutchison
    Sep 17, 2022 at 19:20

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