How to control the conformation when simulating the protein-DNA docking?

Dear all,
I was trying to simulate the T4 ligase interacting with a single stranded DNA. The simulation was successfully completed, but the result was not satisfied. The problem is the simulated result made the DNA went through the side of T4 ligase and it should went into the reaction center of ligase (like a tunnel).
I am wondering if there is any way to control the relative conformation between DNA and ligase to make the result reasonable? You can check result from ID:173849.


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How did you setup the docking?
What kind of restraints/information did you provide?