# protein-DNA docking problem

**URL:** <https://ask.bioexcel.eu/t/protein-dna-docking-problem/3030>\
**Category:** HADDOCK\
**Created:** [June 2, 2021, 9:36am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-problem/3030 "2021-06-02T09:36:20Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Gunj19784](https://avatars.discourse-cdn.com/v4/letter/g/90ced4/32.png) [@Gunj19784](https://ask.bioexcel.eu/u/Gunj19784)\
**Post date:** [June 2, 2021, 9:36am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-problem/3030/1 "2021-06-02T09:36:21Z")

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Hi all,

I am trying to dock 1 protein molecule to a DNA molecule in HADDOCK2.4. I am facing the following issues:

1. Haddock is not taking the both the strands of DNA as a single input and I had to specify both DNA chains as two different molecules. Is it normal? or I am making a mistake.

2. In total I have 3 molecules now to dock to each other. In the Input parameter tab, for each molecule, 2 windows are being shown to input active and passive residues. So I filled the parameters as:  
-For Protein (molecule 1): I selected the active residues to bind to DNA strand (A) and set the partner selection as 2. The I selected the same residues for strand DNA strand (B) in the second window and set the partner selection as 3.

- For DNA strand A (molecule 2): I selected the active bases that bind to Protein 1 and set the partner selection as 1. Then I selected the whole DNA Strand as active residues that bind the molecule 3 (DNA strand B) and set the partner selection as 3.

For DNA strand B (molecule 3): I selected the active bases that bind to Protein 1 and set the partner selection as 1. Then I selected the whole DNA Strand as active residues for the molecule 2 (DNA strand A) and set the partner selection as 2.

But after this, I am still stuck at this page without any error message. I guess I am missing to input some information but don’t know where.  
Please help!!

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 2, 2021, 9:58am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-problem/3030/2 "2021-06-02T09:58:49Z")

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> I am trying to dock 1 protein molecule to a DNA molecule in HADDOCK2.4. I am facing the following issues:
> 
> 1. Haddock is not taking the both the strands of DNA as a single input and I had to specify both DNA chains as two different molecules. Is it normal? or I am making a mistake

Renumber the second strand such as there is not overlap in residue numbering.  
E.g. by shifting the number by a fixed amount using for example our pub-tools web server  
Then submit it as a single molecule

Which should make you next questions unnecessary 🙂

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**Author:** ![Gunj19784](https://avatars.discourse-cdn.com/v4/letter/g/90ced4/32.png) [@Gunj19784](https://ask.bioexcel.eu/u/Gunj19784)\
**Post date:** [June 2, 2021, 10:54am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-problem/3030/3 "2021-06-02T10:54:02Z")

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Thank you so much. It worked. 🙂