GLYCANS working?

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to
Hi all,
is the server to generate PDB up and working? If not, could one those produce proper topology for HADDOCK:


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:

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…

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?

Yes for the 2.4 server

local version too?

Yes of course :slight_smile:

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?

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.