When MD simulation, all water molecules are excluded inside protein (except binding with cofactors). Now my protein has no cofactors, but I want to know how the protein behave once water inside the pocket. However, when the beginning step of MD simulation, all water molecules are deleted. So how can I put one or two water molecules inside the pocket to make MD simulation?
Depending on the software, you can make one or more water molecules part of the protein. Alternatively, you can let the simulation run in explicit solvent and observe water entering the protein.
As allready stated, it depends on the software you're using, but usually, just add the molecules to your coordinate file and assign a different group to it. In most cases you can use the same kind of pair/many body potentials for the water molecule.
If you use amber, you can just run explicit PBC simulations and watch water enter the active site. check amber web page to see a tutorial. you can then use WATCLUST to analyze the structure of water in the protein active
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