[gmx-users] Protein-Ligand Docking?

Justin A. Lemkul jalemkul at vt.edu
Tue May 12 00:18:35 CEST 2009

Chih-Ying Lin wrote:
> HI
> When i visualize the MD trajectory, the protein and ligand are closed by.
> But, I don't know if ligand really DOCK on the protein.

"Docking" cannot be accomplished by Gromacs.  If you wish to determine whether 
or not your ligand or protein are favorably associated, it is up to you to 
quantify whatever is important in your system (distances, hydrogen bonds, etc).


> Please tell me how to define the successful docking.
> Thank you
> Lin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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