# Glycan breaks after topoaa

**URL:** <https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710>\
**Category:** HADDOCK\
**Tags:** haddock\
**Created:** [May 29, 2025, 9:37am UTC](https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710 "2025-05-29T09:37:24Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![marcosgly](https://avatars.discourse-cdn.com/v4/letter/m/a183cd/32.png) [@marcosgly](https://ask.bioexcel.eu/u/marcosgly)\
**Post date:** [May 29, 2025, 9:37am UTC](https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710/1 "2025-05-29T09:37:24Z")

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Hi,  
I’m trying to dock a series of glycans to a glycan receptor. Some of these are chemically modified so I cannot use the glycam webserver to construct these and I have to use rdkit to construct them. My input glycan looks good, but after the topoaa step all of the pdbs generated split my trisaccharide into its single sugar units. Any idea what could be happening here?  
Thank you!

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**Author:** ![marco.giulini](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco.giulini/32/961_2.png) [@marco.giulini](https://ask.bioexcel.eu/u/marco.giulini)\
**Post date:** [May 29, 2025, 9:54am UTC](https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710/2 "2025-05-29T09:54:27Z")

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Hi @marcosgly  
When is this happening?  
if your monosaccharides do not belong to the list of supported carbohydrates ([HADDOCK Web Server - Settings](https://rascar.science.uu.nl/haddock2.4/library)), it’s better to treat the full glycan as a ligand (see an example here [haddock3/examples/docking-protein-ligand/docking-protein-ligand-test.cfg at main · haddocking/haddock3 · GitHub](https://github.com/haddocking/haddock3/blob/main/examples/docking-protein-ligand/docking-protein-ligand-test.cfg)), i.e., providing topology and parameters.

Best,  
Marco

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<div class="post-metadata">

**Author:** ![marcosgly](https://avatars.discourse-cdn.com/v4/letter/m/a183cd/32.png) [@marcosgly](https://ask.bioexcel.eu/u/marcosgly)\
**Post date:** [May 29, 2025, 10:27am UTC](https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710/3 "2025-05-29T10:27:13Z")

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Hi Marco,  
Thanks for the quick reply! The trisaccharide is already broken up in the output of topoaa, the very first step in my config file. I have pseudo set the glycan label for the modified monosaccharide unit to match the HADDOCK-accepted labels. The glycosidic bond between the other two,unmodified glycans is also broken up however. I thought the strength of this glycan approach was to better model the flexibility of glycans within haddock, not sure I can do the same elsewhere and then feed topology and parameter; or do you think that’s quite easily done?  
Anyways, I have attached PDB files for the starting glycan (glycan\_ready) and the topoaa output (glycan\_ready\_haddock).  
[glycan\_ready.pdb](https://ask.bioexcel.eu/uploads/short-url/xw09YVojh3yDZxlDqvi6SDvsI9k.pdb) (7.8 KB)  
[glycan\_ready\_haddock.pdb](https://ask.bioexcel.eu/uploads/short-url/Y2sDNp0cakGbCSMLnwAtdmfatF.pdb) (7.5 KB)

Thank you!  
Marcos

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<div class="post-metadata">

**Author:** ![marco.giulini](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco.giulini/32/961_2.png) [@marco.giulini](https://ask.bioexcel.eu/u/marco.giulini)\
**Post date:** [May 30, 2025, 3:13pm UTC](https://ask.bioexcel.eu/t/glycan-breaks-after-topoaa/5710/4 "2025-05-30T15:13:54Z")

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hi, I checked the PDB file..for HADDOCK it’s impossible to model such a molecule: although the residue names are part of the library of supported libraries, the atom names do not match, so HADDOCK cannot guess the linkages or calculate any energy..the naming should match the standard OPLS/CHARMM topology (see for example [https://charmm-gui.org/?doc=open\_toppar&filename=top\_all36\_carb.rtf](https://charmm-gui.org/?doc=open_toppar&filename=top_all36_carb.rtf) or directly the HADDOCK topology [haddock3/src/haddock/cns/toppar/carbohydrate.top at main · haddocking/haddock3 · GitHub](https://github.com/haddocking/haddock3/blob/main/src/haddock/cns/toppar/carbohydrate.top))

To answer to your question, HADDOCK’s ability to model the flexibility of the glycan will not be influenced by whether you provide or not additional topology/parameters. Those are simply used within HADDOCK to calculate forces and energies for molecules that HADDOCK doesn’t recognize 🙂

Best  
Marco