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
Hi all,
is the server to generate PDB 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
or
https://glycam.org/gag/
Best
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
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?
Merci
Yes for the 2.4 server
local version too?
Yes of course 
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?
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.