[Chimera-users] Parse error Chimera

[Elaine Meng]

Hi Maja,
The short answer is that I have no idea.  Although you start the calculation from Chimera, it uses an autodock prep script and then sends the file to a webserver running Autodock Vina.  Autodock and Autodock Vina are not developed by our group, and the web server is not run by our group.

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

I can’t even try anything unless you provide me the model.   If the model has hydrogens in it, you could try first deleting all hydrogens, e.g. Chimera command:

delete H

and then in the Receptor options you can try “Add hydrogens in Chimera” as “true” and if that doesn’t work, delete hydrogens again, and try it with “false”

If none of those work, it may not be possible to include NAP in your calculation if you use this interface. You may need to get Autodock Vina directly from its website and run it directly (not using Chimera):
<http://vina.scripps.edu/>

I do not know the details of what they recommend if you want to include cofactors in your receptor.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 14, 2019, at 5:25 PM, Dorfner, Maja <maja.dorfner at fau.de> wrote:
> 
> To whom it may concern,
> 
> Using Swissmodel, I have constructed a model based on an original PDB file.
> NAP is part of this model. The docking works when the option of either "Ignore chains of non-standart residues" or "Ignore all non-standart residues" is chosen as false. The Problem is that in the PDBQT file of the receptor shows that NAP was not considered during the docking, making the Substrate float either within the NAP or to far from it. The docking worked fine with the original PDB file but not with the newly modeled one.
> 
> Could the problem be that the NAP is a separate chain?
> I have already tried to erase the H before using AutoDock Vina.
> 
> Here is the Reply log:
> Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more information
> 
> Application stderr
> -----
> 
> 
> Parse error on line 3578 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
> -----
> Application stdout
> -----
> #################################################################
> # If you used AutoDock Vina in your work, please cite:          #
> #                                                               #
> # O. Trott, A. J. Olson,                                        #
> # AutoDock Vina: improving the speed and accuracy of docking    #
> # with a new scoring function, efficient optimization and       #
> # multithreading, Journal of Computational Chemistry 31 (2010)  #
> # 455-461                                                       #
> #                                                               #
> # DOI 10.1002/jcc.21334                                         #
> #                                                               #
> # Please see http://vina.scripps.edu for more information.      #
> #################################################################
> 
> Detected 4 CPUs
> Reading input ... -----
> 
> Thank you for your patience.
> 
> Sincerely,
> Maja Dorfner