Cyclizing .pdb of a linear chain.

[Anonymous]

I am trying to take a .pdb structure that I generated (of a non-canonical peptoid backbone) and cyclize it in order to conduct GenKIC analysis and find favored configurations.

I tried creating the residues with PeptideStubMover, but the coordinates were considerably out of place, such that a given residue was connecting atoms several angstroms off and at angles that made no sense.

I am now trying to work with a premade .pdb structure, link the N- and C-termini, then use an .xml to set up the GenKIC rules.

Whenever I run the command:

/Rosetta/main/source/bin/rosetta_scripts.default.macosclangrelease   @CycE18flags.txt

The errors are as follows:

ERROR: No match found for unrecognized residue at position 18

Looking for upper-terminal residue with 3-letter code: 314

ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 433

0   libutility.dylib                    0x00000001189c3a1b print_backtrace(char const*) + 59

1   libutility.dylib                    0x00000001189c3847 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 887

2   libcore.3.dylib                     0x0000000116df8984 core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types() + 6148

3   libcore.3.dylib                     0x0000000116df5756 core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&) + 54

4   libcore.5.dylib                     0x000000011584aaf5 core::import_pose::build_pose_as_is(std::__1::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&) + 293

5   libcore.5.dylib                     0x0000000115848e62 core::import_pose::build_pose(std::__1::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&) + 210

6   libcore.5.dylib                     0x0000000115848b3d core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType) + 2861

7   libcore.5.dylib                     0x00000001158477bd core::import_pose::pose_from_file(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType) + 93

8   libcore.5.dylib                     0x0000000115845f64 core::import_pose::pose_from_file(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool, core::import_pose::FileType) + 68

9   libprotocols.1.dylib                0x00000001153fd65a protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 1434

10  libprotocols.1.dylib                0x00000001153d8cc4 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 2452

11  libprotocols.1.dylib                0x00000001153d77c5 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 357

12  libprotocols.1.dylib                0x00000001153b5622 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66

13  rosetta_scripts.default.macosclangrelease 0x000000010fd35c24 main + 836

14  libdyld.dylib                       0x00007fff8e9625ad start + 1

15  ???                                 0x0000000000000002 0x0 + 2

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job ‘CycE18_0001’

Error:

[ERROR] EXCN_utility_exit has been thrown from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 433

ERROR: No match found for unrecognized residue at position 18

Looking for upper-terminal residue with 3-letter code: 314

Error: Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: CycE18_0001

protocols.jd2.JobDistributor: no more batches to process…

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds

Error: ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error:

---

I made sure that 314 is uncommented in the residue_types.txt file in database.

I am trying to figure out how to allow the bond1 function in my .xml file to be run without this problem.

 

Anyone who can help with this, I would greatly appreciate it.

 

Thank you.

 

[Anonymous]

I sent this along to Vikram (the relevant developer)

[Anonymous]

Vikram says “peptoids don’t work with genKIC, these are known issues, we are working on fixing them”

[Anonymous]

Is there a loop-modeling methodology that accepts peptoids?

Specifically one that will allow generation of cyclic peptoids?

[Author]

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