ADL: Could not find any conformations completely within the search space...

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ADL: Could not find any conformations completely within the search space...

Samantha Rose Goldstein

   Hi all,
   I am running a flexible docking on Vina and the following error message has
   been produced:
   "WARNING: Could not find any conformations completely within the search
   space.
   WARNING: Check that it is large enough for all movable atoms, including
   those in the flexible side chains."
   Under  the  assumption the gridbox coordinates were too restrictive, I
   expanded the box and the error showed again.  I made flexible the residues
   responsible  for ligand binding and for the conformation change of the
   activated receptor.  My gridbox only covers the binding region.  Does "large
   enough for all movable atoms" mean that the box needs to cover the flexible
   residues involved in conformation change as well?
   Any insight on i) what the error message means and ii) what I should do to
   correct this would be much appreciated.
   Thank you,
   Sam Goldstein
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Re: ADL: Could not find any conformations completely within the search space...

Ruth Huey

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Samantha Rose Goldstein [[hidden email]]
Sent: Tuesday, July 14, 2015 9:26 AM
To: [hidden email]
Subject: ADL: Could not find any conformations completely within the search space...

   Hi all,
   I am running a flexible docking on Vina and the following error message has
   been produced:
   "WARNING: Could not find any conformations completely within the search
   space.
   WARNING: Check that it is large enough for all movable atoms, including
   those in the flexible side chains."
   Under  the  assumption the gridbox coordinates were too restrictive, I
   expanded the box and the error showed again.  I made flexible the residues
   responsible  for ligand binding and for the conformation change of the
   activated receptor.  My gridbox only covers the binding region.  Does "large
   enough for all movable atoms" mean that the box needs to cover the flexible
   residues involved in conformation change as well?

>> Yes!
>> SO increase the size of your gridbox to cover all the possible locations of moving atoms in your flexible residues too


   Any insight on i) what the error message means and ii) what I should do to
   correct this would be much appreciated.
   Thank you,
   Sam Goldstein
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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Re: ADL: Could not find any conformations completely within the search space...

jpc356
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In reply to this post by Samantha Rose Goldstein
If you couldn't find any confirmations you may want to check your macromolecule and ligand .pdb files. I would re-download and prepare them again as something may have gone wrong.

The grid box should be as small as possible to cover the pocket but no smaller. If you cut part of the pocket out with the grid dimensions you will get inaccurate results. On the other hand, if you make it to big, accuracy will decrease since the spacing between points will be larger. (Think of small versus large grid paper - it's a density issue). If you do increase the Angstrom value I would increase the exhaustiveness of the search.

I strongly believe that this is an issue with either your setup or files since you expanded the box and the same issue resulted. If you want, take a look at: https://www.youtube.com/watch?v=ZiuqSzqcD7M

That is a video tutorial that I created for AutoDock. If you continue to have this error please respond back and/or try to use PyRx as it automates nearly the entire workflow. If the ligand and macromolecule are publicly available, and you're okay with it, post or message me the IDs of the files and I'll run it on a known functioning setup and see if the issue persists!

-John Cahill
John Cahill
JPC356@Drexel.Edu
Undergraduate Researcher at Drexel University, Class of 2018

My posts do not reflect the views or knowledge base of Drexel University nor are they affiliated with the university.