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IDProjectCategoryView StatusDate SubmittedLast Update
0000124Rosetta[All Projects] Crashpublic2012-10-03 12:572012-10-05 20:53
Reportermomeara 
Assigned Toptconway 
PrioritynormalSeveritycrashReproducibilityalways
StatusclosedResolutionno change required 
PlatformAll platformsOSAnyOS VersionAny
Product VersionTrunk 
Fixed in Version 
Summary0000124: CartBondedEnergy crashes on 1aye due to issue with residue connections
DescriptionScoring with the cart bonded term crashes on 1aye. I looked briefly at it and it the problem occurs at core/scoring/methods/CartBondedEnergy.cc:412

where res is residue 2, THR, and neighb_res is residue, GLU_p:NTermFull.

It crashes with

rosetta_scripts.linuxclangdebug: src/utility/vectorL.hh:352: const_reference utility::vectorL<1, core::chemical::ResidueConnection, std::allocator<core::chemical::ResidueConnection> >::operator[](const index_type) const: Assertion `static_cast< size_type >( i - l_ ) < super::size()' failed.

Program received signal SIGABRT, Aborted.
0x00007fffe79e33a5 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
        in ../nptl/sysdeps/unix/sysv/linux/raise.c

Steps To Reproducedownload structure and run the command line listed below.
Additional InformationHere is the back trace where it crashes

#0 0x00007fffe79e33a5 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007fffe79e6b0b in __GI_abort () at abort.c:92
0000002 0x00007fffe79dbd4d in __GI___assert_fail (assertion=0x7ffff7a22360 "static_cast< size_type >( i - l_ ) < super::size()", file=<optimized out>, line=352, function=<optimized out>) at assert.c:81
0000003 0x00007ffff7800135 in utility::vectorL<1l, core::chemical::ResidueConnection, std::allocator<core::chemical::ResidueConnection> >::operator[] (this=0x171e980, i=2) at src/utility/vectorL.hh:352
0000004 0x00007ffff382f4da in core::chemical::ResidueType::residue_connection (this=0x171e140, i=2) at src/core/chemical/ResidueType.hh:800
0000005 0x00007fffec4b95ed in core::scoring::methods::BondAngleDatabase::lookup (this=0x108e3ea0, pose=..., res=..., atm1=2, atm2=1, atm3=-1, Ktheta=@0x7fffffff9c18, theta0=@0x7fffffff9c10) at src/core/scoring/methods/CartesianBondedEnergy.cc:412
0000006 0x00007fffec4c2d01 in core::scoring::methods::CartesianBondedEnergy::residue_pair_energy (this=0x108d6f60, rsd1=..., rsd2=..., pose=..., sf=..., emap=...) at src/core/scoring/methods/CartesianBondedEnergy.cc:1085
0000007 0x00007fffec006dc6 in core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies (this=0x10e38ca0, pose=...) at src/core/scoring/symmetry/SymmetricScoreFunction.cc:555
0000008 0x00007fffec00250e in core::scoring::symmetry::SymmetricScoreFunction::operator() (this=0x10e38ca0, pose=...) at src/core/scoring/symmetry/SymmetricScoreFunction.cc:171
0000009 0x00007ffff21be5e3 in protocols::features::StructureScoresFeatures::compute_energies (this=0x1086a270, pose_in=..., relevant_residues=..., emap=...) at src/protocols/features/StructureScoresFeatures.cc:231
0000010 0x00007ffff21bd61d in protocols::features::StructureScoresFeatures::insert_structure_score_rows (this=0x1086a270, pose_in=..., relevant_residues=..., struct_id=..., db_session=<optimized out>) at src/protocols/features/StructureScoresFeatures.cc:274
0000011 0x00007ffff21bd327 in protocols::features::StructureScoresFeatures::report_features (this=0x1086a270, pose=..., relevant_residues=..., struct_id=..., db_session=...) at src/protocols/features/StructureScoresFeatures.cc:204
0000012 0x00007ffff2109a26 in protocols::features::ReportToDB::report_features (this=0x10855770, pose=..., struct_id=..., relevant_residues=...) at src/protocols/features/ReportToDB.cc:656
0000013 0x00007ffff21091f4 in protocols::features::ReportToDB::apply (this=0x10855770, pose=...) at src/protocols/features/ReportToDB.cc:612
0000014 0x00007fffee8ec64b in protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair (this=0x10d70950, pose=..., mover_pair=...) at src/protocols/rosetta_scripts/ParsedProtocol.cc:411
0000015 0x00007fffee8e6831 in protocols::rosetta_scripts::ParsedProtocol::sequence_protocol (this=0x10d70950, pose=..., mover_it_in=...) at src/protocols/rosetta_scripts/ParsedProtocol.cc:472
0000016 0x00007fffee8e6119 in protocols::rosetta_scripts::ParsedProtocol::apply (this=0x10d70950, pose=...) at src/protocols/rosetta_scripts/ParsedProtocol.cc:141
0000017 0x00007fffee967672 in protocols::jd2::JobDistributor::go_main (this=0x896fc0, mover=<optimized out>) at src/protocols/jd2/JobDistributor.cc:479
0000018 0x00007fffee93d781 in protocols::jd2::FileSystemJobDistributor::go (this=0x896fc0, mover=<optimized out>) at src/protocols/jd2/FileSystemJobDistributor.cc:187
0000019 0x0000000000402824 in main (argc=4, argv=0x7fffffffe2e8) at src/apps/public/rosetta_scripts/rosetta_scripts.cc:85
TagsNo tags attached.
Application(s) Affectedall applications that use CartBondedEnergy
Command Line Usedscore_jd2.linuxclangdebug -score:weights score12_cart -s 1ayeFH.pdb.gz
Developer OptionsConfirmed As Bug
Fixed in SVN Version51537
Attached Filesgz file icon 1ayeFH.pdb.gz [^] (127,752 bytes) 2012-10-03 12:57

- Relationships

-  Notes
(0000115)
ptconway (Developer)
2012-10-05 20:53

not a cart_bonded issue

zero occupancy bug with ResidueConnection - fix by altering zero occupancy field of Nterm LEU backbone nitrogen from 0.00 to 1.00

- Issue History
Date Modified Username Field Change
2012-10-03 12:57 momeara New Issue
2012-10-03 12:57 momeara Status new => assigned
2012-10-03 12:57 momeara Assigned To => ptconway
2012-10-03 12:57 momeara File Added: 1ayeFH.pdb.gz
2012-10-05 20:53 ptconway Fixed in SVN Version => 51537
2012-10-05 20:53 ptconway Note Added: 0000115
2012-10-05 20:53 ptconway Status assigned => closed
2012-10-05 20:53 ptconway Resolution open => no change required


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