[gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

bharat gupta wrote:
> Hi Justin,
> 
> I am having following doubts regarding umbrella sampling of phosphate 
> ion binding to my protein .
> 
> 1. As per the tutorial, I need to fix an immobile reference. In my case 
> which region do I have to fix as my protein consists of one single 
> chain. Since  I am studying the binding and unbinding of ion, shall I 
> fix the ion fixed. If it's so, then do I have to give a different chain 
> name for it as my complex doesnot chain name for ion/ligand.
> 

You don't need an immobile reference just because my tutorial did.  I had a 
particular need to do so.  For your purpose, I highly doubt it's necessary. 
You're looking at small molecule-protein interactions, not protein-protein 
interactions.

> 2. What should be the size of box and how do I know where to place the 
> protein's COM in box (the precise location).
> 

The absolute COM is somewhat irrelevant; all distances during pulling are 
relative.  You can place the protein in a certain location in the box for 
convenience if you like.  The box size must be greater than twice the pull 
distance, as explained in the tutorial.  The amount that you wish to pull will 
dictate both the location of the protein and the box size.

-Justin

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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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