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.
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab