Molecular Dynamics Of Glycosylated Protein

Question

[srikrish.sree]

I need to perform a MD simulation of a glycosylated protein. I tried using GROMACS 3.2. But it is not able to read the glycosylation. Suggest me some reliable MD platforms to use. Can higher version of GROMACS be used??

Answer 1

[João Rodrigues]

You need to generate a topology for the carbohydrate molecule. Try the PRODRG server or this one: http://haddock.chem.uu.nl/enmr/services/GLYCANS/