# How can i do protein and DNA-ligand docking

**URL:** <https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145>\
**Category:** HADDOCK\
**Created:** [June 27, 2016, 3:31pm UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145 "2016-06-27T15:31:18Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Maolin\_Wang](https://avatars.discourse-cdn.com/v4/letter/m/a183cd/32.png) [@Maolin\_Wang](https://ask.bioexcel.eu/u/Maolin_Wang)\
**Post date:** [June 27, 2016, 3:31pm UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/1 "2016-06-27T15:31:18Z")

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The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2)

Dear administrator or anyone,

I am doing the docking between protein and a DNA linked with ligand. Can HADDOCK do this kind of docking?

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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 28, 2016, 4:13am UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/2 "2016-06-28T04:13:53Z")

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A covalently bound ligand will be problematic. But if you treat it as non-covalent it should work.  
The ligand should have HETATM in the PDB file. And I would define a few distance restraints between your ligand and the DNA to keep it in place (upload those as unambiguous distance restraints in the _distance restraints_ menu (requires expert access).

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**Author:** ![Maolin\_Wang](https://avatars.discourse-cdn.com/v4/letter/m/a183cd/32.png) [@Maolin\_Wang](https://ask.bioexcel.eu/u/Maolin_Wang)\
**Post date:** [June 28, 2016, 5:16am UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/3 "2016-06-28T05:16:03Z")

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Thanks very much amjjbonvin. There is also a problem. The error message said the DG residule is not supported.

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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 28, 2016, 5:38am UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/4 "2016-06-28T05:38:10Z")

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Use a three letter code for nucleic acid bases, i.e. GUA instead of DG

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**Author:** ![Ashleigh](https://avatars.discourse-cdn.com/v4/letter/a/4bbf92/32.png) [@Ashleigh](https://ask.bioexcel.eu/u/Ashleigh)\
**Post date:** [November 7, 2016, 7:37pm UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/5 "2016-11-07T19:37:16Z")

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How so you convert from the two letter code to 3 letter code?

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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:** [November 7, 2016, 10:02pm UTC](https://ask.bioexcel.eu/t/how-can-i-do-protein-and-dna-ligand-docking/145/6 "2016-11-07T22:02:59Z")

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Edit the file and replace the names… make sure not to mess up column positions