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Topology and parameter files for sugar residues in glycoproteins

From: "Andersen, Kim Vilbour (KVA)" <>
To: <>
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I'm trying to model a glycoprotein with Modeller and would like to include the glyco-part in the modelling.

I'm fighting with the creation of topology files (and parameter files) creating the topology of the different involved sugar residues as well as patch residues to create the relevant bonds.

Has anybody out there done this already and are willing to share?

I'm mainly interested in N-acetylglucosamine, N-acetylgalactosamine, Mannose, Galactose and Sialic acid as well as the relevant patchings.

Any input will be appreciated,



Kim Vilbour Andersen, PhD
Principal Scientist
Agern AllÈ 1
DK-2970 H¯rsholm