[Dock-fans] Double bonds

James Foster (PG Research) j.r.foster at dundee.ac.uk
Fri Dec 16 12:56:10 PST 2016

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,


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<http://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<http://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.


On Thu, Dec 15, 2016 at 6:52 PM, James Foster (PG Research) <j.r.foster at dundee.ac.uk<mailto:j.r.foster at dundee.ac.uk>> wrote:


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?

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