# Recognition problem after glycan sulfation

**URL:** <https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641>\
**Category:** HADDOCK\
**Created:** [November 1, 2023, 9:11am UTC](https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641 "2023-11-01T09:11:32Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![xinxin](https://avatars.discourse-cdn.com/v4/letter/x/ccd318/32.png) [@xinxin](https://ask.bioexcel.eu/u/xinxin)\
**Post date:** [November 1, 2023, 9:11am UTC](https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641/1 "2023-11-01T09:11:32Z")

</div>

Hello,  
I am a webserver user of Haddock2.4 and I want to make a sulfated modified glycan and protein binding, but I look at the manual supported by the carbohydrate does not have a name for the sulfated group, please ask me what I should do.

thank you for your support.  
best  
Francesco

---

<div class="post-metadata">

**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:** [November 1, 2023, 4:11pm UTC](https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641/2 "2023-11-01T16:11:15Z")

</div>

If you want to dock a sulfonated carbohydrate to your protein, then define the glycan as HETATM giving it a unique residue name and unique atom names.

We followed that strategy for example to dock heparin.  
This might require some manual editing of your glycan file.

---

<div class="post-metadata">

**Author:** ![xinxin](https://avatars.discourse-cdn.com/v4/letter/x/ccd318/32.png) [@xinxin](https://ask.bioexcel.eu/u/xinxin)\
**Post date:** [November 13, 2023, 12:58pm UTC](https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641/3 "2023-11-13T12:58:54Z")

</div>

Hello, I have a question, how to represent sulfonated groups in the pdb file?

HETATM 1 S SO4

HETATM 2 OS1 SO4

HETATM 3 OS2 SO4

HETATM 4 OS3 SO4

This doesn’t seem to work. I looked at the HADDOCK2.4 library and I didn’t see any way to chemically modify carbohydrates.

---

<div class="post-metadata">

**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:** [November 13, 2023, 3:05pm UTC](https://ask.bioexcel.eu/t/recognition-problem-after-glycan-sulfation/4641/4 "2023-11-13T15:05:22Z")

</div>

We do not have support for sulfonated glycans with the supported glycans listed on the website (see: [https://bianca.science.uu.nl/haddock2.4/library](https://bianca.science.uu.nl/haddock2.4/library))

One solution is to define you full glycan as HETATM. If you have multiple units, it should be defined as a single residue with non-overlapping atom names.

But this will only work if you are docking a glycan (and not dealing with a glycosylated protein as in that case the connectivity to the protein would not be created).