ADL: Vina: atom not found in this branch

Ruth Huey rhuey at
Tue Jun 18 14:05:12 PDT 2013

Hi Jacob,
Here is the file...
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


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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