Error during single state design

[Anonymous]

Hi,

During single state design of protein the following error is encountered after relaxing the structure at the fixed backbone design stage  and also by design iterated by backrub motion.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job 4MUI_relax_design_0010

File: src/core/conformation/Conformation.hh:499

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

Any help in resolving the problem will be appreciated.

With regards

Suji george

 

[Anonymous]

Unfortunately, that “The sequence position requested was 0.  Pose numbering starts at 1.” message is one of the more common ones you’ll run into in Rosetta. We use “0” as a general “desired residue can’t be found” code, and if the person writing a bit of code doesn’t consider it (or you run into an edge case/condition which is outside what they designed for), you’ll get that message.

To help track down what’s really at issue, we would need to see a backtrace which leads up to that error. If that’s not in the tracer output itself, it likely can be found in the ROSETTA_CRASH.log that’s in your working directory. Posting that here could potentially help us figure out what might be going on.

[Anonymous]

 

Thanks for the prompt response. Please find the backtrace

BACKTRACE:

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2e6) [0x7ff1d0cb70b6]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_b.6.so(core::conformation::Conformation::residue(unsigned long) const+0xff) [0x7ff1d2bc776f]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.4.so(protocols::analysis::InterfaceAnalyzerMover::set_pose_info(core::pose::Pose const&)+0x7c) [0x7ff1cdabd58c]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.4.so(protocols::analysis::InterfaceAnalyzerMover::apply_const(core::pose::Pose const&)+0x144) [0x7ff1cdad20e4]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.4.so(protocols::analysis::InterfaceAnalyzerMover::apply(core::pose::Pose&)+0x15) [0x7ff1cdabd1c5]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x29a) [0x7ff1d1e21e0a]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x7ff1d1e2208b]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1c6) [0x7ff1d1e230f6]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbe4) [0x7ff1d1f0c864]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x1bb) [0x7ff1d1f0e74b]

/home/niv/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x56) [0x7ff1d1ef5146]

rosetta_scripts.default.linuxgccrelease(+0x21ae) [0x55dd50f231ae]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7ff1d0037b97]

rosetta_scripts.default.linuxgccrelease(+0x24fa) [0x55dd50f234fa]

protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/conformation/Conformation.hh:499

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job 4HKX_relax_design_0010

File: src/core/conformation/Conformation.hh:499

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

protocols.jd2.JobDistributor: [ ERROR ]

protocols.jd2.JobDistributor: [ WARNING ] 4HKX_relax_design_0010 reported failure and will NOT retry

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

protocols.jd2.JobDistributor: 10 jobs considered, 10 jobs attempted in 452 seconds

Error: [ ERROR ] Exception caught by rosetta_s

Thanking you and anticipating a response soon

[Anonymous]

So the error is in the InterfaceAnalyzerMover, specifically in the set_pose_info() function. The only call to Conformation::residue() there is when looking at the residues upstream and downstream of a particular jump, which indicates to me that there’s some issue with the jump.

How are you setting up your InterfaceAnalyzer in your RosettaScripts XML? Specifically, what method are you using to set which chains are part of your interface? If you don’t have that set correctly – if you’re asking for an interface which doesn’t actually exist, for example – you can run into this sort of issue.

If you’re specifying the interface with the “jump” attribute, I’d suggest trying to use the “interface” attribute, which uses the designation like “HL_AB”, where the underscore separates the chain letters which are on each side of the interface.

If you don’t actually have multiple chains you’re looking at the interface between – if you’re doing design on a monomer, for instance, then that would be your problem. The InterfaceAnalyzerMover is specifically for interfaces, and isn’t intended for (won’t work on) monomers or structures where there isn’t an interface between two chains.

[Anonymous]

I am setting the InterfaceAnalyserMover  in the rosettascript .XML as shown below

<InterfaceAnalyzerMover name=”analyze” scorefxn=”REF2015” fixedchains=”H,L” pack_separated=”1” pack_input=”0” packstat=”0“/>

I am using PDB complex with three chains H, L and E, where chains H and L are treated as monomer and chain E as the binding partner.

The  fixedchains=”H, L”  option is consistantly giving the error. However removal of  this option from the script result in running of the full protocol, however the sequence of the designed residue at the interface and the binding energy doesnot correlate  with test results. Any help would be appreciated

Thanking you

[Anonymous]

Oh, it looks like you’re using Rosetta 3.10. There’s unfortunately a bug with the InterfaceAnalyzer in Rosetta 3.10. Using a more recent release (like Rosetta 3.11 or a weekly on or after the 2018.42 one) should avoid this issue.

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