# Carbohydrate not attached to ASN residue during docking **URL:** \ **Category:** HADDOCK\ **Tags:** haddock, support\ **Created:** [March 8, 2025, 6:59pm UTC](https://ask.bioexcel.eu/t/carbohydrate-not-attached-to-asn-residue-during-docking/5466 "2025-03-08T18:59:06Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![norm](https://avatars.discourse-cdn.com/v4/letter/n/f475e1/32.png) [@norm](https://ask.bioexcel.eu/u/norm)\ **Post date:** [March 8, 2025, 6:59pm UTC](https://ask.bioexcel.eu/t/carbohydrate-not-attached-to-asn-residue-during-docking/5466/1 "2025-03-08T18:59:07Z")
I have a BGLCNA carbohydrate that is attached to my protein through a N-linked glycosylation (to asparagine). It originally shows up in the PDB file as BGLC, which caused errors, so I changed it to GLC, and the job ran fine. I got good results, but I realized that the carbohydrate had drifted a few angstroms away in the docked poses. I realized that HADDOCK did not recognize the N-linkage. I was wondering if anyone knows a way to create that bond manually. I wanted to create a restraint but since the carbohydrate is a HETATM, I don’t think I can specify the carbon in the sugar molecule. I was able to just build the bond back while preparing the system for MD simulations, but since the covalent bond is now 4 angstrom, I’m not sure if this will be corrected during minimization/equilibration. Any advice is appreciated. ---
**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:** [March 8, 2025, 10:00pm UTC](https://ask.bioexcel.eu/t/carbohydrate-not-attached-to-asn-residue-during-docking/5466/2 "2025-03-08T22:00:37Z")
This is strange as this should be supported. Could you share your input PDB? ---
**Author:** ![norm](https://avatars.discourse-cdn.com/v4/letter/n/f475e1/32.png) [@norm](https://ask.bioexcel.eu/u/norm)\ **Post date:** [March 8, 2025, 10:52pm UTC](https://ask.bioexcel.eu/t/carbohydrate-not-attached-to-asn-residue-during-docking/5466/3 "2025-03-08T22:52:53Z")
Hi I found a support email from another post ([haddock.support@gmail.com](mailto:haddock.support@gmail.com)). I sent my PDB structure there. ---
**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:** [March 9, 2025, 2:41pm UTC](https://ask.bioexcel.eu/t/carbohydrate-not-attached-to-asn-residue-during-docking/5466/4 "2025-03-09T14:41:15Z")
Hi Norman I took a look at your glycan. First you seem to need NDG instead of GLC since it is a N-acetylated one. See: [HADDOCK Web Server - Settings](https://rascar.science.uu.nl/haddock2.4/library) I modified accordingly the PDB file and run a refinement server test. All looks good and the glycan is connected to ASN (see the direct email you got with the files attached).