ADL: Vina: atom not found in this branch

Oleg Trott trott at scripps.edu
Wed Jun 19 10:02:13 PDT 2013


As I recall, there was a bug in AutoDock Tools that would sometimes
make it generate bad "BRANCH/ENDBRANCH" entries in the PDBQT file.
(That bug may have been fixed since then in the most recent versions)

For example, "BRANCH 4 34" means that there is a rotatable bond from
atom #4 to atom #34, where atom #4 is in the parent branch, and atom
#34 is in the daughter branch. If atom #34 does not exist in the
daughter branch, AutoDock Vina will, quite justifiably, refuse to work
with such a file, alerting the user to the problem. AutoDock 4 might
not be as thorough in checking its input.

On Wed, Jun 19, 2013 at 2:00 AM, Douglas Houston
<DouglasR.Houston at ed.ac.uk> wrote:
> Hi all,
>
> I too found this error a while ago, I should have posted it. I recall that
> Autodock docks staurosporine without complaint ...
>
> cheers,
>
> Doug
>
>
>
> Quoting Ruth Huey <rhuey at scripps.edu> on Tue, 18 Jun 2013 14:05:12 -0700:
>
>> Hi Jacob,
>> Here is the file...
>>    -Ruth
>> ________________________________________
>> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On
>> Behalf Of Lucrezi, Jacob D [jlucrezi3 at gatech.edu]
>> Sent: Tuesday, June 18, 2013 12:34 PM
>> To: autodock at scripps.edu
>> 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  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
>
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>
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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