# Docking protein with peptide ensemble

**URL:** <https://ask.bioexcel.eu/t/docking-protein-with-peptide-ensemble/4474>\
**Category:** Uncategorized\
**Created:** [August 31, 2023, 11:16pm UTC](https://ask.bioexcel.eu/t/docking-protein-with-peptide-ensemble/4474 "2023-08-31T23:16:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [August 31, 2023, 11:16pm UTC](https://ask.bioexcel.eu/t/docking-protein-with-peptide-ensemble/4474/1 "2023-08-31T23:16:43Z")

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Hi  
I am docking a protein with an ensemble of peptides, how can I be sure that HADDOCK reads them all? I don’t see their name in run.cns

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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:** [September 1, 2023, 7:44am UTC](https://ask.bioexcel.eu/t/docking-protein-with-peptide-ensemble/4474/2 "2023-09-01T07:44:44Z")

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Check the begin directory - there you should find PDBs for all your peptides and all combinations of protein - peptide

Your it0 sampling should of course be larger than the number of combinations