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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