[Chimera-users] Autodock Vina plugin

[Eric Pettersen]

Hi,
	Autodock Vina is getting tripped up by hydrogen names it doesn't expect. Try this: delete all hydrogens with the command (Favorites→Command Line) "del H". Then under "Receptor options" in the AutoDock Vina panel change "Add hydrogens in Chimera" to "false". 

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 4, 2022, at 7:27 AM, Enrico Martinez via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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
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