# How to specify only certain cysteines to form disulfide bonds? **URL:** \ **Category:** HADDOCK\ **Tags:** haddock\ **Created:** [April 29, 2025, 1:17pm UTC](https://ask.bioexcel.eu/t/how-to-specify-only-certain-cysteines-to-form-disulfide-bonds/5641 "2025-04-29T13:17:59Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Hoa\_Thanh\_Le](https://avatars.discourse-cdn.com/v4/letter/h/5f9b8f/32.png) [@Hoa\_Thanh\_Le](https://ask.bioexcel.eu/u/Hoa_Thanh_Le)\ **Post date:** [April 29, 2025, 1:17pm UTC](https://ask.bioexcel.eu/t/how-to-specify-only-certain-cysteines-to-form-disulfide-bonds/5641/1 "2025-04-29T13:17:59Z")
Hello, I have a PDB file where not all CYS residues form disulfide bonds. I learnt from [this question](https://ask.bioexcel.eu/t/how-to-deal-with-disulfite-bond-in-haddock3/5638) that HADDOCK3 will evaluate all CYS combinations for potential disulfide bonds. Is there a way to specify only certain cysteines to form disulfide bonds? Thank you. Hoa ---
**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:** [April 29, 2025, 2:02pm UTC](https://ask.bioexcel.eu/t/how-to-specify-only-certain-cysteines-to-form-disulfide-bonds/5641/2 "2025-04-29T14:02:38Z")
Not possible, but if they are not close in space this should not be an issue. ---
**Author:** ![Hoa\_Thanh\_Le](https://avatars.discourse-cdn.com/v4/letter/h/5f9b8f/32.png) [@Hoa\_Thanh\_Le](https://ask.bioexcel.eu/u/Hoa_Thanh_Le)\ **Post date:** [April 29, 2025, 3:18pm UTC](https://ask.bioexcel.eu/t/how-to-specify-only-certain-cysteines-to-form-disulfide-bonds/5641/3 "2025-04-29T15:18:04Z")
Dear Mr. Bonvin, Thank you for your prompt reply. I hope that unwanted disulfide bonds won’t be an issue to the docking score. Best regards, Hoa