An enzyme is responsible for degradation of a specific dye. Is it possible to use MD simulation to understand the mechanism.
How I would approach it: need to dock before, after, and the transition states. Make an electrostatic map of the contact areas before and after degradation. Then ask an organic chemist to figure out the transition states, or try to figure it out myself. Dock the transition states. But I don't really know this so I'm gonna come back to check this question.
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how do i get the transition states?
I don't know what the dye, the enzyme, the products, or the docking states look like so I don't know how they are interacting - amino acid side chains in contact, which parts of them, what parts of the dye they are in contact with. So I can't answer your question. Even if I knew, I'm not an organic chemist so I won't know if I'm correct. Again, I don't actually know this stuff so you should check with someone else.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749658/pdf/pone.0148191.pdf http://www.pnas.org/content/105/26/9059.full.pdf http://www.sciencedirect.com/science/article/pii/S0168165606000800