Hi!
I want to dock an ion (Cl-) to my protein model using autodock vina. The error is as follows:
WARNING atoms have no bonds....BUILDING THEM!!!
WARNING atoms have no bonds....BUILDING THEM!!!
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_ligand4.py", line 207, in
attach_singletons=attach_singletons)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 1019, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py", line 789, in __init__
self.aromCs = self.ACM.setAromaticCarbons(molecule)
File "/usr/lib/python2.7/dist-packages/AutoDockTools/atomTypeTools.py", line 210, in setAromaticCarbons
assert len(molecule.allAtoms.bonds[0])
AssertionError
it is pretty obvious, that there are no bonds within single ion molecule. So, is it possible to dock an ion with Vina? Or shall I use other software?
Can you, perhaps, create Cl-X molecule, where "X" is a dummy atom with zero charge and van der Waals radius? If not, how about docking of a small chlorine-containing molecule, e.g. CH3Cl?
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I would also check all X-ray crystal structures of the protein and its close homologs for chloride ions, ligands and ordered water molecules, and I would assess each potential chloride binding site manually:
http://bmcstructbiol.biomedcentral.com/articles/10.1186/s12900-014-0019-8
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And I would attempt predicting/evaluating the chloride binding sites via molecular dynamics simulations of the protein in solution (water, sodium ions, chloride ions).
You can dock a single atom to a receptor using Autodock rather than Autodock Vina.
this is not the easy job. Lot of things have to be taken care (problem with gasteiger charge charge, parameterization etcccc) even with commerialised softwares too).
Could you please let me know, what is your object? May be I can help you some other way.
I need this docking for creating initial system for MD. Docking via MD doesnt work, the ion floats away. Also, there are no crystal structure templates.
Anyway, the problem was only about generating pdbqt file of ligand. All I had to to do was to remove sanity check checking number of bonds. Without it only warning about not detecting any bonds is printed. Another workaround is to prepare ligand pdbqt file manually.
Thanks for your responses!
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