Member Site Forums Rosetta 3 Rosetta 3 – General Patches for post-translational modifications Reply To: Patches for post-translational modifications


    What does rosetta do with the p-ser now? Crash out on unrecognized residue, throw out the P and O atoms…?

    If you look at rosetta_database/chemical/residue_type_sets/fa_standard/patches.txt, you’ll see the patch is enabled by default (not commented out). This means Rosetta ought to be able to recognize it automatically. Try playing with the atom and residue names in your phosphoserines in the PDB file to make them match what Rosetta expects. It looks like the atom names are ” P “, ” O1P”, etc, as in the patch file, and the expected 3 letter name is still SER. Read the patch and params file to play around with it.

    If that fails, the function to add patches is probably

    pose::Pose & pose,
    VariantType const & variant_type,
    Size const seqpos

    in src/core/chemical/util.*