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PostPosted: Tue Jan 17, 2017 5:13 pm 
Millimolar User
Millimolar User
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Joined: Tue Jan 17, 2017 4:57 pm
Posts: 2
Hi everyone,
this is my problem:
I'm using Chimera 1.11.2 and the integrated Autodock Vina script.
I have a known pdb model and generated several structural models of similar protein sequences using the integrated MODELLER script.
Since the pdb model also contains a FAD cofactor, I let the MODELLER script integrate FAD (non-water HETATM) as well into my models.

However, after model generation I want to do substrate/product docking studies with my known pdb model and the generated structural models, respectively, using the Autodock Vina script.

When I use the known pdb model as receptor, everything works fine.
But when I'm using the generated structural models as receptors, I always get following error msg:
"Parse error on line 8481 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 when I generate the structural models without integrating the FAD into my model, the AutoDockVina script also works fine.
Within the file an excerpt looks like this:
HETATM 8482 HO3B FAD 524 62.332 67.414 -32.163 1.00 0.00 0.229 Ho
HETATM 8483 HO2B FAD 524 61.112 67.370 -35.434 1.00 0.00 0.218 Ho
HETATM 8484 1H6A FAD 524 68.689 67.444 -38.650 1.00 0.00 0.157 HD
HETATM 8485 2H6A FAD 524 67.993 65.870 -38.318 1.00 0.00 0.157 HD

I found that AutoDock would need a "HD" instead of a Ho in the pdbqt file? Is this correct?
The problem here is that AutoDock vina generates the receptor.pdbqt file itself. So why does it generate a file with a Ho parameter when it cannot read it? How can i circumvent this problem? I cannot just change the "Ho" to "HD" within the pdbqt file since the AutodockVina script always generates a new receptor.pdbqt file at the beginning.

I hope you could understand my problem and maybe you can help me!

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Translated by MaĆ«l Soucaze © 2009