[Chimera-users] Autodock Vina plugin

[Enrico Martinez]

... I guess it might be related to the executables of VINA since the
local path was empty

I tried to put there the full path to vina (which works well from the
terminal on my mac)
/usr/local/bin/vina
and it gaved me 5 docking solutions
BINGO!!
:-)
one question:
how I could remove only protein's Hydrogen atoms using Chimera's
command line (keeping them on the ligand)???

ср, 5 янв. 2022 г. в 09:30, Enrico Martinez <jmsstarlight at gmail.com>:
>
> Thank you very much, Eric!
> I actually tried to remove all hydrogens from the protein and ligand
> and in that case there was an error related to prepare_ligand4.py
>
> then I removed hydrogens only from the protein (keeping them for the
> ligand) and got new error:
> Service 'local:' is unavailable.  See Reply Log for more details.
> Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto
> adding gasteiger charges to peptide
> 'Deleting non-standard residues: from test.receptor
> Wrote test.ligand.pdb into /Users/gleb/Desktop/docking_tuto
> Traceback from web application request:
> Traceback (most recent call last):
>   File "/Applications/Chimera.app/Contents/Resources/share/WebServices/appWebService.py",
> line 48, in _initApp
>     self.backend = Backend(service, url)
>   File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_local.py",
> line 59, in __init__
>     % self.exePath)
> UserError: "" is not an executable
> Service 'local:' is unavailable.  See Reply Log for more details.
>
> вт, 4 янв. 2022 г. в 19:20, Eric Pettersen <pett at cgl.ucsf.edu>:
> >
> > 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
> > > _______________________________________________
> > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >