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Error with simple_cycpep_predict protocol while using a native pdb file

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Error with simple_cycpep_predict protocol while using a native pdb file
#1

Hello Rosetta devs,

 

I'm not sure that this is the right place to post a bug. If not, please let me know where to post.

 

I compiled both Rosetta 3.10 (and then 2019.07 release), and faced the following error when trying to predict cyclic peptides with terminal disulfide bonds using the simple_cycpep_predict protocol.

To be more specific, my peptide has a non-terminal CYS residue at the C-term, and I was using the

-in:file:native

 flag. When computing without a native structure, no error occured.

The backtrace pointed to the set_up_terminal_disulfide_cyclization_mover function (see attached file).
 

Looking at the source code, I found that the last residue index was sent to the set_up_terminal_disulfide_cyclization_mover function instead of the last CYS residue index. As a dirty fix, I added the following line

last_disulf_res = find_last_disulf_res( native_pose );

 at line 2481 and changed the next line from

set_up_cyclization_mover( termini, native_pose, true, last_res );

to 

set_up_cyclization_mover( termini, native_pose, true, last_disulf_res );

 in the main/source/src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc file.

 

This solved my issue but I haven't further tested this fix (especially, I haven't tested the other cyclization types).

 

HTH,

 

Florent

 

AttachmentSize
error.txt3.93 KB
Post Situation: 
Tue, 2019-03-26 10:05
Florent Langenfeld

Hi, Florent.  If you can send me your inputs at vmulligan@flatironinstitute.org, I'll fix that bug permanently.  Thanks!

Tue, 2019-03-26 11:23
vmulligan