Hello users, I am trying to simulate Hydrogen and Oxygen gas diffusion pathways in a protein. First I have simulated the protein in a water bath for 50 ps . Now I want to simate it in a box containing either only gas molecule or both gas+water molecule. I have used genbox to replace some water molecule randomly with hydrogen gas molecule. The problem is that when I am prepairing the top file fo this system it is not identifying the hydrogen gas molecule. Please tell me the way by which I can do this simulation. Kindly also tellme about some papers related to this work. Sincerely Vipul Gupta
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