cartesian_ddg cannot mutate intact disulfide bonds

[KapilMcinerney]

Hi All,

I'm currently performing mutagenesis of a protein and calculating ddG using cartesian_ddg. However, i've noticed that i cannot seem to mutate a cysteine if its apart of a disulfide bond (free cysteines work perfectly). The program just doesn't perform the mutation and outputs structures with the WT residue. Looking at the cartesian.out file i've noticed it gives this error message for every amino acid involved in a disulfide bond

core.pose.util: [2025- 3- 4 12:37:22:] [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 420 BRANCH 1

Is there a way around this so i can mutate an intact disulfide bond + calculate ddG or does the software just not allow it?

Cheers! Kapil

[roccomoretti]

The issue with mutation of cysteines in disulfides is that just mutating the one residue leaves the other side of the disulfide being "half a disulfide" rather than being a cysteine. -- Theoretically the mutational process could recognize this and update the other side, but it's likely that it hasn't been coded for this edge case.

The workaround is to set things up in the input PDB such that the residues being mutated are free cysteines, rather than disulfides.