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Questions regarding the Grid box / search area
http://mgl.scripps.edu/forum/viewtopic.php?f=12&t=3348
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Author:  Jonas S [ Mon Dec 12, 2016 6:13 pm ]
Post subject:  Questions regarding the Grid box / search area

I am currently doing docking experiments of docking a quite sizable ligand to a receptor. My question is if i need to make space for the ligand in my grid box. I currently have just made the grid box big enough to contain all residues i believe to be involved in the binding. I have yet to have a good result, but i have had a few results were the ligand were docked inside the receptor. This has led me to question why there have not been some similar bad bindings where the ligand were docked closer to the molecular surface and i realized this may be due to my grid box size not allowing this?

Below is the link to two pictures, my question is wether or not my ligand could be docked outside the smaller gridbox (the whole ligand would not fit inside the gridbox), or i would need to use the larger gridbox in order to make docking possible.

http://imgur.com/a/7FFK9
(Sorry didn't figure out how to link them directly in post and were to big to attach to post)



Of course i'd rather use the larger box anyway but due to the size and some problem with the computer network the smaller box already takes about 100hours to dock and time is of somewhat limited.

Author:  bioinfoswamy [ Sat Feb 04, 2017 6:22 am ]
Post subject:  Re: Questions regarding the Grid box / search area

Dear my friend,

I have gone through your problem.It is the problem with ligand size and preparation of grid size. In the given images, ligand is missing. Provide the grid box along with ligand and protein with surface. Then it will be easy to understand the binding surface.

Wish you all the best..

Still you face the problem drop a mail to me at k.swamy@dpu.edu.in

bye


Dr.K.V.Swamy, M.Sc., Ph.D
Associate Professor,
Bioinformatics Research Group,
Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,
Dr.D.Y.Patil Vidyapeeth,
Tathawade, Pune
India.
PIN:411033
www.biotech.dpu.edu.in
Phone:+91 20 67919444 Extn: 9449

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