I am using simple_cycpep_predict in design mode to find derivatives of a peptide for disulfide cyclization. For the -cyclic_peptide:allowed_residues_by_position option I am using the following file:
DEFAULT ILE LEU ARG TRP SER ARG LYS LEU PRO CYS VAL SER
1 ILE # Only ILE at this position.
2 ILE LEU VAL # Only branched, small, hydrophobic residues at this position.
3 ARG LYS # Only positively-charged residues at this position.
4 TRP PHE TYR CYS # Only hydrophobic, bulky, slightly polar, or CYS residues at this position.
5 SER CYS # CYS in this position
6 ARG LYS GLU ASP CYS # Only negative, positive residues, or CYS at this position.
But I get the following error:
[ ERROR ] UtilityExitException
ERROR: Error in core::pack::task::PIKAA::add_base_name_to_keep(): The base name "ARG" was added more than once.
Is there anything wrong with the format of the residues file?