[Chimera-users] Autodock Vina plugin

[Enrico Martinez]

Dear Chimera Users,
First Happy New Year to you and your families!

I am trying to perform protein-ligand docking using UCSF Chimera 1.16v
installed on my iMAC Big Sur.
Using the pdb of the receptor and mol2 of the ligand (that I have
already tested with VINA 1.2.3!) I got the following error:
Model 1 (receptor.pdb) appears to be a protein without secondary
structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
No SEQRES records for receptor.pdb (#1) chain A; guessing terminii instead
Chain-initial residues that are actual N terminii: #1 SER 1.A
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii:
Chain-final residues that are not actual C terminii: #1 THR 304.A
278 hydrogen bonds
Removing spurious proton from 'C' of #1 THR 304.A
Hydrogens added
Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto
adding gasteiger charges to peptide
Traceback (most recent call last):
  File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py",
line 395, 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 Hn Hn
Receptor preparation for AutoDock Vina failed; please look in Reply
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.

So here are my questions:
1) May this error be related to the version of OSX installed on my
imac (I can not run MGL tools on the Big Sur for instance) ??

2) Alternatively may I use the ADT scripts integrated in the Chimera
like prepare_receptor4.py for my scripting purposes (outside of the
UCSF Chimera) on the same iMAC machine ?

Many thanks in advance!
Cheers
Enrico