Hi Sangita!
For glycoproteins, you should be using the glycam force field, plus the instructions you'll find on the amber handbook on how to construct a glycan.
Alternatively, the very friendly glycam developers have an on-line GUI for adding whatever glycans you like best to your protein, and directly produce either pdb files you can use to calculate topology and coordinate files. They can also directly produce those same files, but for me, I've always had some weird setup, which I could not input into their GUI.
For your enjoyment, here is their website: http://glycam.org/
All the best,
Manuel
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Received on Mon Aug 04 2014 - 00:00:01 PDT
