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

[bharat gupta]

Hi,

I want to dock a barrel protein with phosphate ion , to look for the sites
where Phosphate ion binds... I searched the gmx list but I didn't find much
related threads..
I want to do the following things...
1) Simulate the binding of phosphate ion with a barrel protein. Here I do
not know where does the ions binds and thats what I want to find through
simulation..
2) After getting the site , I want to look for the binding affinities
between the predicted sites..

I want to know how shall I approach this.. since I don't know how many ions
I have to simulate with the protein..Can anybody help or refer to some
paper??

Regards

-- 
Bharat
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