[gmx-users] Fwd: Simulation of protein with phosphate ion...

bharat gupta bharat.85.monu at gmail.com
Tue May 31 02:01:23 CEST 2011

Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
such a case the movement of ion is very important. As the ion in side the
barrel can quench the fluorescence. That's what I want to track..

On Mon, May 30, 2011 at 4:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> bharat gupta wrote:
>> Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me in
>> determining the binding affinity. So, my first objective can be achieved
>> with it.
>> Then what about the movement of ions into the barrel. Will it be possible
>> to track it with MD coz the movement of ion is very important in my case. I
>> don't want them to enter the barrel rather I want them to be on the surface
>> of the barrel??
> You can implement such restraints, or guide the ion through the channel,
> whichever you prefer.  The literature is rich with studies of the movement
> of ions and small molecules through transporters and channels.
> -Justin
> --
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> Justin A. Lemkul
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> Department of Biochemistry
> Virginia Tech
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