Generally, I am wondering how chemically modified residues work with fragments. Specifically, is there any way to generate fragments for particular residues that have phosphorylation, carbohydrates, acetylations, etc? Second, if there is no way and one passes a fragment library for Rosetta to use, and the residues where these fragments will be built are variants such as SER_phosphorylated, what is Rosetta's behavior? Will it crash or just build the fragments as normal?
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Residue variant types and fragments