[gmx-users] how to describe the change of channel in the MD

Justin Lemkul jalemkul at vt.edu
Wed Jun 19 17:34:32 CEST 2013

On 6/19/13 11:21 AM, aixintiankong wrote:
>   Dear,
>       In the MD, I find that when the ligand keep in the active site , the channel formed by two loops is closed. without the ligand the channel is opened. I don't know how to describe the change of channel. could i describe the channel by calculating the the most narrow distance(mass center) between the residues on the two loops? please give me some adviece. thank you very much!

This question was answered already:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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