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@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