[Dock-fans] Double bonds

Brian Fochtman brianfochtman at gmail.com
Thu Dec 15 19:18:41 PST 2016

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
      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.


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
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