# Docking cyclic peptides using Ligand PDBs

**URL:** <https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633>\
**Category:** HADDOCK\
**Created:** [October 26, 2023, 8:18am UTC](https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633 "2023-10-26T08:18:56Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![jannled](https://avatars.discourse-cdn.com/v4/letter/j/838e76/32.png) [@jannled](https://ask.bioexcel.eu/u/jannled)\
**Post date:** [October 26, 2023, 8:18am UTC](https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633/1 "2023-10-26T08:18:57Z")

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Hello,

I want to dock a cyclic peptide on a target, with the cyclic peptide chain being defined as UNL in the PDB. When using the online Haddock tool, I define the cyclic peptide PDB as Ligand, and turn on the cyclic peptide button (as shown in the picture below). **Question** : Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?

Many thanks

 ![Screenshot 2023-10-26 at 10.16.00](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/0db27c644e6383ad88df3aa40a61e847bff00016.png)

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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:** [October 26, 2023, 9:58am UTC](https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633/2 "2023-10-26T09:58:53Z")

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> ). Question: Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?

No it won’t. This only works with amino acids, i.e. standard supported ones defined as ATOM

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**Author:** ![AhmedEzat](https://avatars.discourse-cdn.com/v4/letter/a/898d66/32.png) [@AhmedEzat](https://ask.bioexcel.eu/u/AhmedEzat)\
**Post date:** [February 4, 2025, 7:24am UTC](https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633/3 "2025-02-04T07:24:41Z")

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Dear Prof. Bonvin,  
Can’t we make docking for cyclic peptides with non natural amino acids?  
Best,  
Ahmed

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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 4, 2025, 7:50am UTC](https://ask.bioexcel.eu/t/docking-cyclic-peptides-using-ligand-pdbs/4633/4 "2025-02-04T07:50:45Z")

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The only one we are supporting are the ones listed on the following page:

[

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[HADDOCK Web Server - Settings](https://rascar.science.uu.nl/haddock2.4/library)  
[science.uu.nl](https://rascar.science.uu.nl/haddock2.4/library)

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[![favicon.ico](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/1/107bb531973837ba0aa1bffdc74d58b781de99e8.png)](https://rascar.science.uu.nl/haddock2.4/library)

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