ADL: Vina: atom not found in this branch

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ADL: Vina: atom not found in this branch

Lucrezi, Jacob D
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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Re: ADL: Vina: atom not found in this branch

Oleg Trott
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 <[hidden email]> 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
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



--
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com

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Re: ADL: Vina: atom not found in this branch

Ruth Huey
In reply to this post by Lucrezi, Jacob D
Hi Jacob,
Here is the file...
   -Ruth
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Lucrezi, Jacob D [[hidden email]]
Sent: Tuesday, June 18, 2013 12:34 PM
To: [hidden email]
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 ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

staurosporine1_hs.pdbqt (4K) Download Attachment
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Re: ADL: Vina: atom not found in this branch

HOUSTON Douglas
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 <[hidden email]> on Tue, 18 Jun 2013 14:05:12 -0700:

> Hi Jacob,
> Here is the file...
>    -Ruth
> ________________________________________
> From: [hidden email] [[hidden email]] On  
> Behalf Of Lucrezi, Jacob D [[hidden email]]
> Sent: Tuesday, June 18, 2013 12:34 PM
> To: [hidden email]
> 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

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: ADL: Vina: atom not found in this branch

Oleg Trott
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
<[hidden email]> 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 <[hidden email]> on Tue, 18 Jun 2013 14:05:12 -0700:
>
>> Hi Jacob,
>> Here is the file...
>>    -Ruth
>> ________________________________________
>> From: [hidden email] [[hidden email]] On
>> Behalf Of Lucrezi, Jacob D [[hidden email]]
>> Sent: Tuesday, June 18, 2013 12:34 PM
>> To: [hidden email]
>> 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
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



--
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com
________________________________________________
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