[Dock-fans] Double bonds

Brian Fochtman brianfochtman at gmail.com
Fri Dec 16 14:19:36 PST 2016


Can you send your mol2 files?

On Fri, Dec 16, 2016 at 3:56 PM, James Foster (PG Research) <
j.r.foster at dundee.ac.uk> wrote:

> Hi Brian,
>
>  Thanks very much for the reply. I tried preparing the molecule with your
> script, running a flexible docking algorithm and then post processing the
> output file your script but the double bonds still come out as trans instead
> of remaining cis? Maybe it's not right to use a flexible docking algorithm
> on a molecule containing a long alkyl chain with double bonds?
>
>
> Thanks again,
>
> James
> ------------------------------
> *From:* Brian Fochtman <brianfochtman at gmail.com>
> *Sent:* 16 December 2016 03:18:41
> *To:* James Foster (PG Research)
> *Cc:* dock-fans at docking.org
> *Subject:* Re: [Dock-fans] Double bonds
>
> Hi Jim,
>      There are a couple ways to to change this behavior within DOCK.  The
> method I prefer is as follows:
>
>      I've attached a script that should be used to pre and post process
> your molecules.
>
>       1.   python     2014.05.16_cyclize_db.py      input.mol2
> temp_for_docking.mol2
>       2.   run dock as you normally would except specify
> "temp_for_docking.mol2" from above as the ligand_atom_file
>       3.   python      2014.05.16_cyclize_db.py
> output_scored.mol2       final_output_scored.mol2
>
>
>      What this process does is lock all double bonds in the molecule in
> the original conformations.  Running the script the second time cleans up
> the output file.  One disadvantage of this process is that RMSDs have to be
> calculated after the face on final_output_scored.mol2.    Let me know if
> you have any questions or need help getting the script running.
>
> -Brian
>
>
> On Thu, Dec 15, 2016 at 6:52 PM, James Foster (PG Research) <
> j.r.foster at dundee.ac.uk> wrote:
>
>> Hello,
>>
>> I’ve tried using rigid and flexible docking to dock a molecule containing
>> a cis c-c double bond. After running the dock the conformation of the bond
>> turns into trans? Please do you know of any solution to correct this?
>> Thanks,
>> Jim
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> _______________________________________________
>> Dock-fans mailing list
>> Dock-fans at docking.org
>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>
>>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20161216/2f318d44/attachment.html 


More information about the Dock-fans mailing list