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simple_cycpep_predict issue modifying terminal residue

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simple_cycpep_predict issue modifying terminal residue
#1

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.

AttachmentSize
test_pdb.txt21.47 KB
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Thu, 2020-06-25 13:15
JEaston

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.

Mon, 2020-06-29 13:09
vmulligan