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Thanks a lot for your kind reply.
I don’t mean to use Rosetta to produce models with the entire carbohydrate present, but only use part of the carbohydrate for docking.
What I want to do is use Roseeta to judge and dock correctly carbohydrate by itself. Because, if there is no crystal structure, I don’t know which part of the carbohydrate would have H-bond with protein, so neither which part will not have H-bond with protein.
So, I am wondering is it possible for Roseeta make such kind of decision by itself? Or should I combine other kind of methods for further validate such as: MD?