# Protein docking with two ligands, then confusion regarding the output of pdb file results

**URL:** <https://ask.bioexcel.eu/t/protein-docking-with-two-ligands-then-confusion-regarding-the-output-of-pdb-file-results/5838>\
**Category:** HADDOCK\
**Tags:** haddock\
**Created:** [July 31, 2025, 6:52am UTC](https://ask.bioexcel.eu/t/protein-docking-with-two-ligands-then-confusion-regarding-the-output-of-pdb-file-results/5838 "2025-07-31T06:52:44Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Boson](https://avatars.discourse-cdn.com/v4/letter/b/d26b3c/32.png) [@Boson](https://ask.bioexcel.eu/u/Boson)\
**Post date:** [July 31, 2025, 6:52am UTC](https://ask.bioexcel.eu/t/protein-docking-with-two-ligands-then-confusion-regarding-the-output-of-pdb-file-results/5838/1 "2025-07-31T06:52:44Z")

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Hello,

I attempted to perform a simultaneous docking of a protein with ligand A and ligand B using HADDOCK 2.4. I successfully generated the results from HADDOCK. However, when I examined the 3D structure, I found that the two ligand molecules shown in the pdb file were both ligand A. I’m certain that I added two different ligands. Could you please tell me how I should modify my input to obtain the 3D structure diagram of the protein-ligand docking with the two different molecules?

Warm regards

Boson

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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:** [July 31, 2025, 8:05am UTC](https://ask.bioexcel.eu/t/protein-docking-with-two-ligands-then-confusion-regarding-the-output-of-pdb-file-results/5838/2 "2025-07-31T08:05:37Z")

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In HADDOCK, one molecule only has one chain. So if the ligand was part of the protein it will have inherited its chainID.