[Dock-fans] Amide Planarity

James Foster (PG Research) j.r.foster at dundee.ac.uk
Mon Jul 24 15:01:19 PDT 2017

Hi Brian,

Thanks very much for your help! I tried the script and it worked great. I've been using version 6.7 which may explain why I was having difficulty.


From: Brian Fochtman <brianfochtman at gmail.com>
Sent: 24 July 2017 20:14:52
To: James Foster (PG Research)
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] Amide Planarity

Hi James,
   Which version of dock are you using - I've worked on a feature to preserve planarity in amide bonds (that are labeled 'am' in the mol2 file) and believe it may be implemented in the latest version of the code (6.8). If you do not have 6.8 you can use the following work around that I have had some success with:

Use the attached python script on your input ligand file and specify a temporary mol2 file that you will use for docking. Perform docking without a bmp filter using the temporary ligand file. Finally run the same python script on your output. The script attaches and removes 'dummy' atoms which prevent sampling or minimization of torsion angles around double bonds and amides.

      1.   python     2017.07.24_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      2017.07.24_cyclize_db.py<http://2014.05.16_cyclize_db.py/>      output_scored.mol2       final_output_scored.mol2


On Sat, Jul 22, 2017 at 6:46 PM, James Foster (PG Research) <j.r.foster at dundee.ac.uk<mailto:j.r.foster at dundee.ac.uk>> wrote:


I recently tried to dock a molecule containing an amide and noticed it looked wrong. Does anyone know a way of conserving the planarity of amides?



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