I was able to open the file you sent me, and I saw the glycans attached to the protein. I’m affraid to tell you MDWeb didn’t integrate the amber glycam parameters (http://glycam.org/docs/forcefield/parameters-energy-functions/), for different reasons, mainly for the possible atom types incompatibilities with force field versions (please see http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/).
Anyway, I think you were considering using the Coarse-grained methods integrated in MDWeb to obtain dynamic properties of the system, and I have to tell you that all our methods (NMA, DMD, BD) are just working with standard residues, almost all of them with just C-alpha atoms, so even with the right parameters, our CG methods wouldn’t work for your particular problem.
I’m really sorry for that. Thanks for your interest in our tool.