Docking between DNA and a protein

Dear All,

I am docking between a DNA whose backbone is having a bond break (missing oxygen atom between two bases) and a protein molecule. After docking apparently, the resulted DNA molecule is completely restored without any damages.
I don’t want this to happen. I want to understand how the damaged DNA is interacting with protein molecule. I have tried changing the residue numbers; adding certain modifications like adding Hydrogen atom etc. as of now nothing works. Is there any other alternative that I can do to rectify this issue?

Try adding a TER statement after the break in your DNA

I tried that as well. Even after that there is no differnence in the output clusters.

Does not surprise me… What are you expecting?
Does the protein binds close the broken linkage?

I don’t want the damage to be rectified. I expect that the protein go and interact with the damage site without rectifying the damage (somehow haddock adds a phosphate backbone).

Indeed, HADDOCK will add a phosphate at the 3’ end automatically.

No options to prevent that on the server I am afraid.

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