[gmx-users] help regarding simulation

[onetwo]

Hello All,

I want to know one thing that if MD could be used in my case, i have a protein for which crystal structure is known  with a conenzyme bound to it. It is given in literature that related proteins of this family shows large conformational change near the substrate binding region when the substrate binds to the protein.
In absence of the crystal structure, if doing simulation with the protein complexed with the coenzyme and the docked substrate will be useful? , i.e, if this complex with the help of the simulation could be capable of displaying such conformational change ? or what could be the probable limitaions ?

Regards and thanks for your time.
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