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

[bharat gupta]

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
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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