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
EX 1 EX 2
108 H PIKAA K
I need help to make this work.