You are here

simple_cycpep_predict - Design mode - The base name "ARG" was added more than once

5 posts / 0 new
Last post
simple_cycpep_predict - Design mode - The base name "ARG" was added more than once
#1

Hello,

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:

[FILE]: src/core/pack/task/ResfileReader.cc
[LINE]: 708
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::pack::task::PIKAA::add_base_name_to_keep(): The base name "ARG" was added more than once.

[END_MESSAGE]
[END_CRASH_REPORT]

Is there anything wrong with the format of the residues file?

Best

 

Category: 
Post Situation: 
Thu, 2022-08-04 02:57
almeida85

It looks like you have ARG listed twice in the DEFAULT line:

DEFAULT ILE LEU ARG TRP SER ARG LYS LEU PRO CYS VAL SER

Thu, 2022-08-04 07:49
rmoretti

Oh, I see, thanks.

So, if I understood well, the DEFAULT line is the list of amino acids that will be introduced randomly in the non-specified positions, correct?

Thu, 2022-08-04 08:47
almeida85

That's my understanding -- The DEFAULT line is used for any position which isn't explicitly listed otherwise.

Thu, 2022-08-04 09:50
rmoretti

Solved, thanks.

Thu, 2022-08-11 00:58
almeida85