[Chimera-users] [Chimera] Failure preparing structure for Autodock Vina

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 20 08:15:49 PST 2017

Dear Jutapat,
The chimera-users address (CC’d here) is recommended  for questions, for your future reference.  Email to me only might fall through the cracks.

It is hard to tell what the problem is without having your data, but the message says it cannot figure out the atom type of some atom Ha, so maybe the hydrogen atoms in your input structure have weird names or the names are in the wrong columns of the file.

You might try deleting all hydrogens (e.g. command: delete H) before running the tool.  However, if that doesn’t work you probably need to correct some error in your input file (the file format or atom names in the file).
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 20, 2017, at 1:30 AM, Jutapat Romsuk <jutapat_rom at bio.eng.osaka-u.ac.jp> wrote:
> My problem is show below
> Wrote prteinA.receptor.pdb
> Traceback (most recent call last):
>   File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 393, in prepareReceptor
>     execfile(scriptPath, d)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module>
>     delete_single_nonstd_residues=delete_single_nonstd_residues)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__
>     version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__
>     self.addCharges(mol, charges_to_add)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges
>     chargeCalculator.addCharges(mol.allAtoms)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges
>     babel.assignHybridization(atoms)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization
>     a.babel_atomic_number = self.get_atomic_number(a.babel_type)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number
>     (name,_name) )
> ValueError: Could not find atomic number for Ha Ha
> Receptor preparation for AutoDock Vina failed; please look inReply Log to see error messages.
> cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors.
> I would like to know how to fix this problem. Help me please.
> ---------------------------------------------------------------------------------------
> Jutapat ROMSUK
> Biotechnology Global Human Resource Development Program
> Cell Technology Laboratory
> Department of Biotechnology, Graduate School of Engineering, Osaka University
> C2-111, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
> Laboratory phone: +81-6-6879-7423

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