[Chimera-users] running DockPrep and Vina from python

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 3 14:09:30 PST 2017


Hi Anthony,
This is entirely befuddling, because to my knowledge the receptor.pdb file is literally the input to the script that makes the receptor.pdbqt file.  In other words, I don’t see how the script could possibly access the unmodified data.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

However, the script may delete parts of the structure, see the “Receptor options” settings in the manpage linked above.  The receptor prep script is from AutoDock, for more details see: 
<http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-receptor-file-for-autodock4>

Besides setting the prep options appropriately, all I can say is to check the files very carefully, making sure to remove old files from previous runs.  However, I don’t know python, so maybe the others will have some better insights.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 3, 2017, at 5:24 AM, Lee A.G. <A.G.Lee at soton.ac.uk> wrote:
> 
> Hello
> I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1)
> from DockPrep import prep
> model=Midas.open('4iaq.pdb')
> prep(model)
> modelname='4iaq.mol2'
> from WriteMol2 import writeMol2
> writeMol2(model, modelname)
>  
> #VinaRun
> OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq'
> rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true")
>  
> The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering.
> The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering.
> The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1.
>  
> What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don’t have.
> Any help would be very gratefully received.
> Anthony




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