Error with simple_cycpep_predict protocol while using a native pdb file

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- March 26, 2019 at 5:05 pm #3098
  Anonymous
  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
- March 26, 2019 at 6:23 pm #14612
  Anonymous
  Hi, Florent. If you can send me your inputs at vmulligan@flatironinstitute.org, I’ll fix that bug permanently. Thanks!
  - September 21, 2020 at 2:40 pm #15510
    Anonymous
    Hello, Vikram
    
    Have you made any progress on that issue?
    
    Regards,
    
    Florent
  - September 22, 2020 at 10:03 am #15516
    Anonymous
    Hi,
    
    I’ve made some additional tests, and actually, the problem only happens when (1) you ask for a terminal_disulfide cyclization, (2) a pdb file is provided as input and (3) the sequence and input file does NOT end with a cysteine.
    
    When the last residue is a cysteine, everything goes fine…
    
    Hope this help,
    
    Florent
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