Calculate_protein_protein_ddg

[Anonymous]

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
-ignore_unrecognized_res
-out:path:pdb scored_files
-out:path:score results
-nstruct 1

resfile input
NATAA
EX 1 EX 2
USE_INPUT_SC
start
108 H PIKAA K

I need help to make this work.

Thank you

[Anonymous]

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.

[Anonymous]

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

[Author]

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