[Chimera-users] reading output files (pdbqt) from an external vina dock run back into chimera

[Elaine Meng]

Hello Joern,
As far as I can recall, Autodock Vina will (or at least has a choice to) put all the ligand docking results, i.e. multiple poses and/or compounds, in a single pdbqt file.  I don't have the program currently, so I can't say anything specifically about how to control it.

If all you have now is a lot of separate models, you could try opening them all, and then saving them to a single multi-model PDB file and reopening that single PDB file with ViewDock.  However, that would lose all of the extra information in the pdbqt file, certainly the charge/radius columns, and also perhaps all of the scores and other other descriptors output by docking.  Thus it would be better if you could get the single-file output directly from the docking program.

saving PDB files from Chimera
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 19, 2022, at 5:05 AM, Joern Werner via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello 
> 
> is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc.
> I can read individual ligands fine.
> 
> Many thanks Joern
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