ADL: Vina: atom not found in this branch

Douglas Houston DouglasR.Houston at
Wed Jun 19 02:00:51 PDT 2013

Hi all,

I too found this error a while ago, I should have posted it. I recall  
that Autodock docks staurosporine without complaint ...



Quoting Ruth Huey <rhuey at> on Tue, 18 Jun 2013 14:05:12 -0700:

> Hi Jacob,
> Here is the file...
>    -Ruth
> ________________________________________
> From: autodock-bounces at [autodock-bounces at] On  
> Behalf Of Lucrezi, Jacob D [jlucrezi3 at]
> Sent: Tuesday, June 18, 2013 12:34 PM
> To: autodock at
> Subject: ADL: Vina: atom not found in this branch
> Hello,
> I am using AutoDock Vina and trying to dock staurosporine and I  
> receive the following error when I try to run Vina: atom 34 has not  
> been found in this branch.  I made the pdb file for staurosporine in  
> ChemBio3D Ultra and minimized the energy.  I have had no problem  
> with other ligands using the same method.  I even tried downloading  
> a Chemdraw file of staurosporine but I got the same error message.   
> The atom it is referring to is the bridging oxygen.  Any help is  
> appreciated.
> Thank you,
> Jacob Lucrezi
> Georgia Institute of Technology
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Dr. Douglas R. Houston
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Institute of Structural and Molecular Biology
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