Re: [AMBER] Ligand movement in protein cavatiy

From: Jason Swails <>
Date: Mon, 02 Jun 2014 07:47:37 -0400

On Mon, 2014-06-02 at 13:31 +0200, Jurgens de Bruin wrote:
> Hi,
> Thanks for the reply. I apologies for not being clear by using the term
> "movement". I hope this makes it more clear, I have done a docking study
> using Dock6 the results show 2 possible docking sites that are adjacent to
> each-other, I was hoping to show using MD that the ligand would be able to
> move from one docking site to the next.

Again, see if you can apply some sort of geometric definition to
discriminate between the two docking sites. Then you can reduce your
question to one of a comparison of distances, for instance.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 02 2014 - 05:00:04 PDT
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