# Why is my substrate changing? **URL:** \ **Category:** HADDOCK\ **Tags:** haddock\ **Created:** [June 4, 2025, 8:48am UTC](https://ask.bioexcel.eu/t/why-is-my-substrate-changing/5730 "2025-06-04T08:48:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Jana](https://avatars.discourse-cdn.com/v4/letter/j/258eb7/32.png) [@Jana](https://ask.bioexcel.eu/u/Jana)\ **Post date:** [June 4, 2025, 8:48am UTC](https://ask.bioexcel.eu/t/why-is-my-substrate-changing/5730/1 "2025-06-04T08:48:39Z")
Hello, thanks for all the help in previous work. I’m facing a huge issue regarding the refinement of my protein bind to ADP. For some reasons, even though I checked several times that the input document is right, I always get my ADP molecule without the two phosphates and this also shows inside the output document. The refinement deliberately removes the phosphates of my molecule. I don’t know what to do (I reran the job 3 times with changing the chains etc… nothing works). ---
**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:** [June 4, 2025, 9:29am UTC](https://ask.bioexcel.eu/t/why-is-my-substrate-changing/5730/2 "2025-06-04T09:29:52Z")
Can you share your PDB file? ---
**Author:** ![Jana](https://avatars.discourse-cdn.com/v4/letter/j/258eb7/32.png) [@Jana](https://ask.bioexcel.eu/u/Jana)\ **Post date:** [June 4, 2025, 9:33am UTC](https://ask.bioexcel.eu/t/why-is-my-substrate-changing/5730/3 "2025-06-04T09:33:55Z")
I still can’t upload anything because I am “new user” ---
**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:** [June 5, 2025, 8:20am UTC](https://ask.bioexcel.eu/t/why-is-my-substrate-changing/5730/4 "2025-06-05T08:20:36Z")
Try sending it then to bonvinlab.support@uu.nl