# 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

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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

Hello, Vikram

Have you made any progress on that issue?

Regards,

Florent

Mon, 2020-09-21 07:40
Florent Langenfeld

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

Tue, 2020-09-22 03:03
Florent Langenfeld