[gmx-users] simulation of gases diffusion pathways

[vips g]

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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