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

Zirpel, Bastian Bastian.Zirpel at bci.tu-dortmund.de
Wed Jan 18 06:28:47 PST 2017

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

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!



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