Hello,
I’m trying to realize an in silico virtual screening of possible substrates of an Oligosaccharide Dehydrogenase. Everything works well when docking mixed beta1-3/beta1-4 oligoglucans, but when i try to dock branched oligoglucans (with mixed beta1-3/beta1-6) or oligoxylans with alpha1-2 and alpha1-3 these kind of bonds are missing in the final structures. I red from previous discussions that unsupported glycosidic linkages exist so I want to ask you if these bonds are not supported by the Haddock server and the if the problem could be fixed or bypassed somehow. Here are attached the pdb files of the input glycans (the glycans are generated with the Carbohydrate builder tool of Glycam (GLYCAM-Web | Utilities for molecular modeling of carbohydrates) and multiple conformers are generated with ChimeraX in order to account for the flexibility of these substrates). I’m a web server user. Thank you for the support 
G6G_PSIMTI18.pdb (80.5 KB)
G6G3G_PSIMTI108.pdb (707.6 KB)
A2X_PSIMTI6.pdb (22.2 KB)
A3X_PSIMTI6.pdb (22.2 KB)