ADL: SOLVED prepare_ligand4py fails on quaternary nitrogen atoms

Bennion, Brian bennion1 at llnl.gov
Wed Dec 10 09:03:52 PST 2014


Hello All,

After a brief discussion with Stefano, I was able to find the cause of my problem.  It was due to a bug in MolKit in our installed version of mgltools.  I downloaded the latest version of mgltools*latest.tar.gz and ran my problematic ligand through prepare_ligand4.py and all atoms were converted properly to the pdbqt file.

Thanks Stefano

Brian

________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of Bennion, Brian [bennion1 at llnl.gov]
Sent: Tuesday, December 09, 2014 10:26 AM
To: autodock at scripps.edu
Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Hello Doug,

Yes I am aware of this issue at least for a few months now.  I make sure to double check the final output to make sure it is making sense.  Some cases it never works out, others have been easier convert.

Its interesting that there has not been more follow up from the developers in this regard. Since you posted the bug in 2011.

Brian


-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On Behalf Of Douglas Houston
Sent: Tuesday, December 09, 2014 1:41 AM
To: autodock at scripps.edu
Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Be careful using the -p option, it's broken.

http://forums.openbabel.org/Re-openbabel-bugs-710-Gasteiger-partial-charges-and-the-p-option-td4657732.html



Quoting "Bennion, Brian" <bennion1 at llnl.gov> on Tue, 9 Dec 2014
00:39:32 +0000:

> as a post script to the previous email.  babel -ipdb file.pdb
> -opdbqt file.pdbqt -p 7.0 works to convert the file properly.
> However, it removes all the atom names in the conversion process which
> will make my life a little harder down the road.
>
> brian
>
>
> ________________________________________
> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on
> behalf of Bennion, Brian [bennion1 at llnl.gov]
> Sent: Monday, December 08, 2014 4:35 PM
> To: autodock at scripps.edu
> Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms
>
> Thank you for the quick reply.
> The work path I am following uses a pdb file containing all hydrogen
> atoms that has been subjected to energy minimization.
> prepare_ligand4.py -l somefile.pdb is then called.  An error is given
> stating that only 6 of 23 atoms were written.  So I explicitly select
> the quaternary nitrogen as root with -R 4 (the atom index).
> This allows all but six atoms to be converted.  These six atoms are a
> complete branch from the quaternary nitrogen atom.
>
> Which method do want to me to send the file?
>
> brian
>
>
>
>
> ________________________________________
> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on
> behalf of Stefano Forli [forli at scripps.edu]
> Sent: Monday, December 08, 2014 4:28 PM
> To: autodock at scripps.edu
> Subject: Re: ADL: prepare_ligand4py fails on quaternary nitrogen atoms
>
> Brian,
> it would be helpful if you could provide an example of such molecules
> and a description of what the specific issue is (e.g. unrecognized
> rotatable bonds, misplaced hydrogens, etc...).
>
> Without a well-defined structure it is hard to help, but a general
> advice for peculiar molecular structures is to add hydrogens using
> tools that are more sophisticated than AutoDockTools (that's known to
> have problems with some nitrogen-containing structures), then generate
> the PDBQT file with the scripts or the graphical interface.
>
> S
>
>
> On 12/08/2014 04:24 PM, Bennion, Brian wrote:
>>
>> ________________________________
>>
>>
>> Hello,
>>
>> I am wondering if there is a way to help prepare_ligand4.py recognize
>> and properly prepare ligands for docking when they contain a
>> quaternary nitrogen in which two bonds are part of a 6 member ring.
>>
>> Brian
>>
>>
>>
>> ________________________________________________
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>>
>
> --
>   Stefano Forli, PhD
>
>   Staff Scientist
>   Molecular Graphics Laboratory
>   Dept. of Integrative Structural
>    and Computational Biology, MB-112F
>   The Scripps Research Institute
>   10550  North Torrey Pines Road
>   La Jolla,  CA 92037-1000,  USA.
>
>      tel: +1 (858)784-2055
>      fax: +1 (858)784-2860
>      email: forli at scripps.edu
>      http://www.scripps.edu/~forli/
> ________________________________________________
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>
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>
>




_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston

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


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