# Ligand are residues not shown

**URL:** <https://ask.bioexcel.eu/t/ligand-are-residues-not-shown/4983>\
**Category:** HADDOCK\
**Created:** [May 3, 2024, 7:06am UTC](https://ask.bioexcel.eu/t/ligand-are-residues-not-shown/4983 "2024-05-03T07:06:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![JoelLaia](https://avatars.discourse-cdn.com/v4/letter/j/e79b87/32.png) [@JoelLaia](https://ask.bioexcel.eu/u/JoelLaia)\
**Post date:** [May 3, 2024, 7:06am UTC](https://ask.bioexcel.eu/t/ligand-are-residues-not-shown/4983/1 "2024-05-03T07:06:50Z")

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Hi there,

Since I do not know the active sites of my protein, I am following this ab initio tutorial: [HADDOCK2.4 small molecule binding site screening – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/)

Haddock 2.4 does run; however, the ligand that has 39 residues only shows 1 (as in attached image).

How can I solve this problem please?

 ![Imagem WhatsApp 2024-05-02 às 08.44.31_048fcd65](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/e3702f91e0dd48cbc73f69d56d593e950279f6d0.jpeg)

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [May 3, 2024, 7:12am UTC](https://ask.bioexcel.eu/t/ligand-are-residues-not-shown/4983/2 "2024-05-03T07:12:25Z")

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Dear Joel,

Thanks for your interest in using haddock for your research.

Are you sure your ligand has 39 resiudes ?

- If it is the case, then maybe consider it as a peptide or a protein
- If you ligand has 39 atoms, then everything is fine. Indeed, haddock is attributing the residue name `LIG` to ligands in the PDB file, therefore resulting in a single residue representation. Hence, showing `number of residues = 1` is perfectly fine.

With the hope that this answer help you.

Cheers

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**Author:** ![JoelLaia](https://avatars.discourse-cdn.com/v4/letter/j/e79b87/32.png) [@JoelLaia](https://ask.bioexcel.eu/u/JoelLaia)\
**Post date:** [May 3, 2024, 9:24am UTC](https://ask.bioexcel.eu/t/ligand-are-residues-not-shown/4983/3 "2024-05-03T09:24:14Z")

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Dear VGPReys,

It is indeed the second option 🙂 The ligand I am using is GPP with hetatoms, not a peptide, nor a protein.

Thank you for your reply!

Best,  
Joel