# How do I perform a Haddock docking of a peptide with unnatural amino acid?

**URL:** <https://ask.bioexcel.eu/t/how-do-i-perform-a-haddock-docking-of-a-peptide-with-unnatural-amino-acid/3470>\
**Category:** Uncategorized\
**Created:** [February 23, 2022, 3:59am UTC](https://ask.bioexcel.eu/t/how-do-i-perform-a-haddock-docking-of-a-peptide-with-unnatural-amino-acid/3470 "2022-02-23T03:59:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Kalindu](https://avatars.discourse-cdn.com/v4/letter/k/eada6e/32.png) [@Kalindu](https://ask.bioexcel.eu/u/Kalindu)\
**Post date:** [February 23, 2022, 3:59am UTC](https://ask.bioexcel.eu/t/how-do-i-perform-a-haddock-docking-of-a-peptide-with-unnatural-amino-acid/3470/1 "2022-02-23T03:59:33Z")

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Dear all,

I have a peptide with artificial amino acid (modified cysteine) and a linker. I attached the structure of unnatural amino acid and linker  
May I know, is there a way to use Haddock for docking the system.

[IMG\_0240|666x500](https://ask.bioexcel.eu/uploads/short-url/c0hhW16BCOfhfgAaBzWoWjSGygj.jpeg)

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 23, 2022, 7:13am UTC](https://ask.bioexcel.eu/t/how-do-i-perform-a-haddock-docking-of-a-peptide-with-unnatural-amino-acid/3470/2 "2022-02-23T07:13:30Z")

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The list of supported amino acids can be found at:

[https://bianca.science.uu.nl/haddock2.4/library](https://bianca.science.uu.nl/haddock2.4/library)

Yours is not supported.

You could possibly define the addition to the cysteine as an HETATM residue, and define a distance restraint to keep the two sulphur atoms close to each other.  
In that case you should change the residue name of the cysteine to CYC to allow a closer distance to the sulphur