# GLYCANS working? **URL:** \ **Category:** HADDOCK\ **Created:** [June 23, 2022, 3:08pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781 "2022-06-23T15:08:25Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\ **Post date:** [June 23, 2022, 3:08pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/1 "2022-06-23T15:08:26Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.4](http://www.bonvinlab.org/software/haddock2.4) Hi all, is the server to generate PDB [http://haddock.science.uu.nl/enmr/services/GLYCANS/](http://haddock.science.uu.nl/enmr/services/GLYCANS/) up and working? If not, could one those produce proper topology for HADDOCK: [http://legacy.glycam.org/tools/molecular-dynamics/oligosaccharide-builder/download-files](http://legacy.glycam.org/tools/molecular-dynamics/oligosaccharide-builder/download-files) or [https://glycam.org/gag/](https://glycam.org/gag/) Best ---
**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 23, 2022, 3:29pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/2 "2022-06-23T15:29:58Z")
That’s a rather old server - no longer operational (but we do still have it somewhere). Note that HADDOCK can handle glycans in principle. The ones supported can be found at: [https://wenmr.science.uu.nl/haddock2.4/library](https://wenmr.science.uu.nl/haddock2.4/library) ###### _Supported carbohydrates_- A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4 - BGC: beta-D-glucopyranose - BMA: beta-D-mannopyronose - FCA: alpha-D-fucopyranose - FCB: beta-D-fucopyranose - FUC: alpha-L-fucopyranose - FUL: beta-L-fucopyranose - GAL (GLB): beta-D-galactopyranose - GLA: alpha-D-galactopyranose - GLC: alpha-D-glucopyranose - MAN: alpha-D-mannopyranose - NAG: 2-N-acetyl-beta-D-glucopyranose - NDG: 2-N-acetyl-alpha-D-glucopyranose - NGA: 2-N-acetyl-beta-D-galactopyranose - SIA: alpha-N-acetyl neuraminic acid - SIB: beta-N-acetyl neuraminic acid - XYP: beta-D-xylopyranose We also have quite a number of linkages supported, but not all.. ---
**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\ **Post date:** [June 23, 2022, 3:33pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/3 "2022-06-23T15:33:58Z")
Hi Alexandre so as long as I am consistent with the nomenclature, the force field from one of the two servers are fine for HADDOCK, right? Merci ---
**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 23, 2022, 3:50pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/4 "2022-06-23T15:50:23Z")
Yes for the 2.4 server ---
**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\ **Post date:** [June 23, 2022, 4:03pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/5 "2022-06-23T16:03:23Z")
local version too? ---
**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:** [July 6, 2022, 4:17pm UTC](https://ask.bioexcel.eu/t/glycans-working/3781/6 "2022-07-06T16:17:22Z")
Yes of course 🙂 ---
**Author:** ![guvako](https://avatars.discourse-cdn.com/v4/letter/g/3da27b/32.png) [@guvako](https://ask.bioexcel.eu/u/guvako)\ **Post date:** [September 9, 2022, 6:37am UTC](https://ask.bioexcel.eu/t/glycans-working/3781/7 "2022-09-09T06:37:33Z")
Hi, Is it possible to request addition of non-supported monosaccharides for the glycan database? And/or is it possible to perform docking of glycans that are not in the database? ---
**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:** [September 9, 2022, 10:12am UTC](https://ask.bioexcel.eu/t/glycans-working/3781/8 "2022-09-09T10:12:21Z")
You can always request it - if it gets implemented will depend on the complexity and the time available to do it. And to dock non-supported ones, you will have to define them as HETATM, but the glycan should then be a single residue with no overlap in atom naming.