Member Site Forums Rosetta 3 Rosetta 3 – Applications Calculate_protein_protein_ddg

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    • #2132

        Dear Rosetta Users
        I am trying to utilize the calculate_protein_protein_ddg protocol using the mutation_script.xml protocol on rosetta_2014wk52 build.
        However, I am having a problem with mutating chemically modified residue (sulfated tyrosine) into a desired amino acid. I can mutate any non modified canonical amino acid to whichever amino acid I want but not the chemically modified one.

        sample tail of output pdb
        REMARK DesignRes. # modified amino acid mutation attempt
        REMARK DesignRes, 108 H # non modified amino acid mutation attempt

        Here is my current protocol

        rosetta_scripts.linuxgccrelease @flags -database $ROSETTA_DATABASE -overwrite

        flags file input
        -parser:protocol mutation_script.xml # script format and action similar to the demo mutation_script.xml
        -s scored_files/test.pdb
        -out:path:pdb scored_files
        -out:path:score results
        -nstruct 1

        resfile input
        EX 1 EX 2
        108 H PIKAA K

        I need help to make this work.

        Thank you

      • #10823

          The issue you’re running into is that Rosetta is trying to preserve the “sulfated” property of the residue while it is mutating it. Since Rosetta doesn’t know how to make a sulfated lysine, it chokes when you try to do the mutation. The easy fix is to simply make an input PDB which lacks the sulfation on the tyrosine, and use that as your input for mutation.

        • #10882

            Hi kamau,
            I was having a similar issue.Can you post the pdb file that you used?

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