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    Here’s something from the FAQ section on CS-Rosetta’s website:

    “How to use known disulfide bond information in CS-ROSETTA?

    In order to include the known disulfide bond information for the CS-ROSETTA structure prediction, an additional option “-in:fix_disulf disulf.cst” needs to be added to the ROSETTA3.x command line in the script, where “disulf.cst” is a disulfide bond definition file (and must be located in the same working directory unless its full path is provided as well). An example “disulf.cst” file containing a definition of two disulfide bonds (between residues Cys6 and Cys88 and between Cys38 and Cys68) is listed below:

    6 88
    38 68

    Hope that helps.