ADL: prepare_ligand4py fails on quaternary nitrogen atoms

Douglas Houston DouglasR.Houston at ed.ac.uk
Tue Dec 9 01:41:19 PST 2014


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
>>
>>
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
> --
>   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
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>      email: forli at scripps.edu
>      http://www.scripps.edu/~forli/
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> ________________________________________________
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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

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