Hi, I'm trying to use simple_cycpep_predict to model the conformation of a disulfide linked cyclic peptide. The peptide has an amidated C terminus. I've been trying to get the patch Cterm_amidation working however it appears to ignore the patch.
A sample input sequence is:
CYS ALA ALA ALA ALA CYS ALA ALA ALA:Cterm_amidation
And here's my test input script:
../../bin/Rosetta/rosetta_src_2020.08.61146_bundle/main/source/bin/simple_cycpep_predict.default.linuxgccrelease -cyclic_peptide:sequence_file input.txt -cyclic_peptide:cyclization_type "terminal_disulfide" -cyclic_peptide:min_genkic_hbonds 0 -cyclic_peptide:genkic_min_solution_count 1 -cyclic_peptide:genkic_closure_attempts 10000 -out:nstruct 1 -out:file:o a.pdb
Everything appears to run fine but the PDB that I get out isn't amidated and still has the OXT atom. I've attached it for reference as a txt file.
I'm new to Rosetta so I know that I am probably doing something silly. Any help would be appreciated.
I haven't tried this, but it might just be a capitalization issue. Try:
CYS ALA ALA ALA ALA CYS ALA ALA ALA:CTERM_AMIDATION
It's kind of irksome that it fails silently like that, though.