01 January 2013 8 4K Report

I want to study the structure changes of proteins in presence and absence of calcium ion. The calcium concentration would be 400mM and the phenomenon of interest is sec. structure changes, local conformations. The protein in about 300 aa and I am thinking of doing 25ns simulation. I wanted to know how to add the calcium ions to simulation. Can anyone guide me on this topic? Or suggest a protocol in doing so? I am using the following paper as my protocol for simulation. I just want to know how to add calcium ions to simulation.

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