ADL: Vina: atom not found in this branch

Oleg Trott trott at
Tue Jun 18 13:22:24 PDT 2013

This error message implies that the PDBQT file is malformed.

If you paste the file here (I think the mailing list forbids
attachments), and copy the complete error message, I might be able to
check it.

On Tue, Jun 18, 2013 at 12:34 PM, Lucrezi, Jacob D <jlucrezi3 at> wrote:
> 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
> ________________________________________________
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Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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