# DNA-Protein Docking

**URL:** <https://ask.bioexcel.eu/t/dna-protein-docking/4788>\
**Category:** HADDOCK\
**Created:** [February 5, 2024, 3:24pm UTC](https://ask.bioexcel.eu/t/dna-protein-docking/4788 "2024-02-05T15:24:15Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![AlexR](https://avatars.discourse-cdn.com/v4/letter/a/8dc957/32.png) [@AlexR](https://ask.bioexcel.eu/u/AlexR)\
**Post date:** [February 5, 2024, 3:24pm UTC](https://ask.bioexcel.eu/t/dna-protein-docking/4788/1 "2024-02-05T15:24:15Z")

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Hello ,

I am using Haddock on my local machine.

1. Is it possible to dock a DNA PDB to a protein with 2 chains? I am trying to do so after i used pdb\_tidy from pdb tools but i am getting a RuntimeError(reason). Should i combine the 2 chains and if so how can i do it ?
2. Is it possible to do the docking without the tbl file since I dont know which residues are involved in the docking ?

Thank you in advance!

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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:** [February 8, 2024, 3:45pm UTC](https://ask.bioexcel.eu/t/dna-protein-docking/4788/2 "2024-02-08T15:45:51Z")

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> 1. Is it possible to dock a DNA PDB to a protein with 2 chains? I am trying to do so after i used pdb\_tidy from pdb tools but i am getting a RuntimeError(reason). Should i combine the 2 chains and if so how can i do it ?

The forum is searchable 🙂

E.g. [https://ask.bioexcel.eu/t/dealing-with-dimers/42](https://ask.bioexcel.eu/t/dealing-with-dimers/42)

In short you will have to make your dimer a single chain with non-overlapping residue numbering.

Also described for example in:

[

 ![banner_education-thin.jpg](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/9cfac13c84d79c2705cfd715146e27e79620f62a.jpeg)

[Low-sampling antibody-antigen modelling tutorial using a local version of HADDOCK3](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2023/#preparing-the-antibody-structure)  
[bonvinlab.org](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2023/#preparing-the-antibody-structure)

]([Low-sampling antibody-antigen modelling tutorial using a local version of HADDOCK3 – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2023/#preparing-the-antibody-structure))

and

[

 ![banner_software.jpg](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/101cd89bde2cc97d0e01e5c0eede390b5d756cd0.jpeg)

[How to prepare structures for HADDOCK?](https://www.bonvinlab.org/software/bpg/structures/)  
[bonvinlab.org](https://www.bonvinlab.org/software/bpg/structures/)

]([How to prepare structures for HADDOCK? – Bonvin Lab](https://www.bonvinlab.org/software/bpg/structures/))

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<div class="post-metadata">

**Author:** ![AlexR](https://avatars.discourse-cdn.com/v4/letter/a/8dc957/32.png) [@AlexR](https://ask.bioexcel.eu/u/AlexR)\
**Post date:** [February 8, 2024, 4:08pm UTC](https://ask.bioexcel.eu/t/dna-protein-docking/4788/3 "2024-02-08T16:08:36Z")

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Thank you so much Dr. Bonvin !

Searched a bit further and i managed to make it work.  
Enjoyed learning about the software !

Bonne soirée !