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    I think it is normal. Not every disulfide bond can be generated when the positions are not satisfied. You can try to use distance constraints file to add some restrictions during the simulations.

    > Dear all
    > I can get Rosetta to read a file, but in the structures it produces, the disulphides are only sometimes present. I’m specifying four, but I typically only see two or three generated, and not the same ones each time. I suspect the disulphides are simply another term in the overall energy, so sometimes other energetic factors outweigh the lack of a specified disulphide. I have some related questions
    > 1) is this normal behaviour?
    > 2) is it possible to increase the weight on the disulphides?
    > 3) if not, could other constraints be added – SG to SG, say – in order to encourage disulphide formation? If that’s possible, what format would the .cst file take?
    > Many thanks
    > Daniel