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

bharat gupta bharat.85.monu at gmail.com
Tue May 31 01:54:58 CEST 2011

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??

On Mon, May 30, 2011 at 4:48 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> bharat gupta wrote:
>> Thanks for your reply..
>> Actually I came across a paper "Molecular Modeling of the RNA binding
>> N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in Solution
>> with Phosphate ion"... This paper was published in 1996, by Dr. David van
>> der Spoel.. In this paper , they were trying to find out where exactly the
>> phosphate ions bind to the peptide.
>> I thought may be I can try this but in their case it was a peptide and I
>> am dealing with a barrel protein. As u said that I can go for docking and
>> binding site prediction tools.. Since I am having some of docked complexes
>> of my protein with phosphate ion, can I use MD for checking how strong the
>> binding is or does the ion tries to move inside the barrel.
> It sounds like steered MD and umbrella sampling would be useful.  You can
> pull a phosphate ion through the channel if that's of interest.  Otherwise,
> you can pull the phosphates from whatever binding sites you've determined to
> get free energy changes for any of these processes.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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