[Chimera-users] Autodock vina + modeller + ATOM syntax error

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 18 09:00:17 PST 2017


Hi Bastian,
Modeller, Autodock Vina, and the Autodock prep scripts were not developed by our group.  They are just accessed by Chimera.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>

The Autodock receptor prep script is described at the Autodock website (note Autodock Vina is different than Autodock, although they both take pdbqt input):
<http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-receptor-file-for-autodock4>

However, I suspect the problem is in how Modeller processes the FAD.  Maybe the hydrogen atom names are wrong, at least from the perspective of the prep script.

My recommendation is to remove the hydrogens from the Modeller output (delete H in Chimera) and then try running Autodock Vina including the prep script.  I was able to run it successfully using a receptor file from the PDB with an FAD bound to it (5ipy chain A with FAD, I deleted everything else first).  In Chimera’s Autodock Vina dialog, I used the default “Receptor options,” with  “Add hydrogens in Chimera” and everything else set to true except “Ignore all non-standard residues” set to false.  The FAD in the prepped pdbqt file had only HD, no Ho.

HETATM 4408  H1  FAD A 502      26.552  -3.316  20.086  1.00  0.00     0.172 HD
HETATM 4409  H3  FAD A 502      27.485  -7.045  21.398  1.00  0.00     0.173 HD
HETATM 4410 BHO2 FAD A 502      14.098   0.728  12.507  1.00  0.00     0.210 HD
HETATM 4411 BHO3 FAD A 502      14.362   0.888  14.681  1.00  0.00     0.210 HD
HETATM 4412 'HO2 FAD A 502      25.696  -0.004  18.176  1.00  0.00     0.210 HD
HETATM 4413 'HO4 FAD A 502      21.577  -1.368  17.524  1.00  0.00     0.210 HD
HETATM 4414 1H6A FAD A 502      12.988   8.200   9.163  1.00  0.00     0.157 HD
HETATM 4415 2H6A FAD A 502      14.614   7.592   9.094  1.00  0.00     0.157 HD
HETATM 4416 'HO3 FAD A 502      24.108  -3.036  20.486  1.00  0.00     0.210 HD

I hope this helps,
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 Jan 18, 2017, at 6:28 AM, Zirpel, Bastian <Bastian.Zirpel at bci.tu-dortmund.de> wrote:

> Hi everyone,
> I’m using Chimera 1.11.2 on windows.
> I am experience following error after my workflow.
>  
> I fetched a known pdb model from the servers and generated several structural models of similar sequences using the integrated MODELLER script.
> Since my pdb model contains a covalently attached cofactor in the active site, I let MODELLER include non-water HETATM into my structural models as well.
>  
> Afterwards I tried to do substrate/product binding studies with the known pdb model as well as with the generated structural models using the AutoDockVina script.
> However, when I run the script with the known pdb model, everything works fine.
> But when I’m running the script with the structural models, I receive following error msg:
>  
> “Parse error on line 8553 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.”
>  
> It should be noted that this error does not occur if I won’t include non-water HETATM by MODELLER. Makes sense, since having a look at the generated pdbqt file, the FAD lines are generating the error.
>> HETATM 8554 HO3' FAD   525      62.339  60.023 -29.788  1.00  0.00     0.238 Ho
> HETATM 8555 HO2' FAD   525      66.741  58.106 -28.406  1.00  0.00     0.397 Ho
> HETATM 8556 HO3B FAD   525      60.634  66.984 -32.274  1.00  0.00     0.221 Ho
> HETATM 8557 HO4' FAD   525      65.182  62.428 -29.602  1.00  0.00     0.217 Ho
> HETATM 8558 1H6A FAD   525      68.751  67.392 -38.565  1.00  0.00     0.157 HD
> HETATM 8559 2H6A FAD   525      68.156  65.783 -38.183  1.00  0.00     0.157 HD
> HETATM 8560 HO2B FAD   525      62.183  68.217 -34.408  1.00  0.00     0.253 Ho
>>  
> I found that AutoDockVina needs a “HD” instead of a “Ho” entry at these positions? Is this correct?
> So my question is, why is AutoDock vina generating a pdbqt file in the first place which it cannot read properly in the next step?
> How can I prevent this? I cannot just change the pdbqt entries as AutoDockVina will overwrite it again.
>  
> Thanks in advance for any help!
> Bastian




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