# Docking between DNA and a protein
**URL:** https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082
**Category:** Uncategorized
**Created:** [January 23, 2023, 1:04pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082 "2023-01-23T13:04:29Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@Parvathy\_Sarma](https://ask.bioexcel.eu/u/Parvathy_Sarma)
#### Post date: [January 23, 2023, 1:04pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/1 "2023-01-23T13:04:29Z")
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?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [January 23, 2023, 1:35pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/2 "2023-01-23T13:35:33Z")
Try adding a TER statement after the break in your DNA
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### Author:  [@Parvathy\_Sarma](https://ask.bioexcel.eu/u/Parvathy_Sarma)
#### Post date: [January 23, 2023, 1:43pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/3 "2023-01-23T13:43:38Z")
I tried that as well. Even after that there is no differnence in the output clusters.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [January 23, 2023, 2:55pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/4 "2023-01-23T14:55:25Z")
Does not surprise me… What are you expecting?
Does the protein binds close the broken linkage?
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### Author:  [@Parvathy\_Sarma](https://ask.bioexcel.eu/u/Parvathy_Sarma)
#### Post date: [January 23, 2023, 3:18pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/5 "2023-01-23T15:18:09Z")
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).
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [January 23, 2023, 3:56pm UTC](https://ask.bioexcel.eu/t/docking-between-dna-and-a-protein/4082/6 "2023-01-23T15:56:48Z")
Indeed, HADDOCK will add a phosphate at the 3’ end automatically.
No options to prevent that on the server I am afraid.