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    I faced a similar issue because I needed to model statherin
    and to introduce phosphoserines(SEP) in Rosetta forcefield link

    As you see Rosetta has a mode -phospho_ser,
    which if you added in the options,
    you’ll be able to model proteins with SEP(eg 1F8A)
    from Protein Data Bank.
    In order to do this someone needs to add other amino-acid properties
    such as rotamer statistics in Rosetta_database
    and please find some brief comments in

    Right now Rosetta doesn’t support other modified residues
    and there is not a simple recipe which source files to modify,
    in order to model them.
    In the future releases Rosetta will be extended
    to a more general recipe for such modifed amino-acids.


    > Hi,
    > I have started to use RosettaDock for docking a protein (coordinates from
    > crystal structure) to a peptide (coordinates from NMR). The peptide contains
    > 2 sulfated tyrosine residues (named TYS). Rosetta is not being able to
    > recognize these residues and is giving the error message “unrecognized
    > residue: TYS”.
    > How can I address this problem?
    > Thanks in advance.
    > Sincerely,
    > Priyamvada