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Lots of Prepacking Jobs for Snugdock Failing

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Lots of Prepacking Jobs for Snugdock Failing
#1

Hi all, thanks in advance for any help you might have! I'm currently trying to run some antibody-antigen complex dockings via SnugDock. However, when I do the prepacking step, a bunch of the prepacking jobs fail (around 400 out of 1448). It's unclear as to why these fail, as the rest run fine, and I can't determine any differences between the ones that succeed vs the ones that fail. The only hint I can come up with, is that I've used cluspro for global docking and am following up with snugdock; those files produced from the same cluspro run either all succeed or all fail at prepacking, so it must be something to do with the particular structures. I've attached an example pdb file and its flags here; the error I get in ROSETTA_CRASH.log is:

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.36+release.57ac713
[COMMIT_DATE]: 2021-09-12T14:52:42.922397
[APPLICATION]: /dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/bin/docking_prepack_protocol.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-44)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
 -in:path:database=/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/database/ -in:file:s=/dartfs/rc/lab/G/Grigoryanlab/home/coy/AbAgComplexResults/ClusPro_from_AFabAFag_FIXED/7amp_AfAgAfAbmodel.000.23.pdbLH_Afixed.pdb -out:path:all=/dartfs/rc/lab/G/Grigoryanlab/home/coy/AbAgComplexResults/ClusPro_from_AFabAFag_FIXED/prepacked/ -docking:partners=LH_A

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(backtrace_string(int)+0x3a) [0x2b17767c49da]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x51) [0x2b1776802811]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(char const*, int, std::string const&, int)+0xa5) [0x2b17767c9ac5]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::pose::center_of_mass(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&)+0x69d) [0x2b17735bc79d]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::pose::residue_center_of_mass(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> >)+0x70) [0x2b17735bc970]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols_h.5.so(protocols::docking::setup_foldtree(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&, utility::vector1<int, std::allocator<int> >&, core::kinematics::FoldTree&, bool)+0x1093) [0x2b176b3c87f3]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols_h.5.so(protocols::docking::setup_foldtree(core::pose::Pose&, std::string const&, utility::vector1<int, std::allocator<int> >&, bool)+0x6e0) [0x2b176b3cba30]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols_h.5.so(protocols::docking::DockingPrepackProtocol::finalize_setup(core::pose::Pose&)+0x285) [0x2b176b3674c5]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols_h.5.so(protocols::docking::DockingPrepackProtocol::apply(core::pose::Pose&)+0x19) [0x2b176b3676b9]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xc52) [0x2b177082c352]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x2b177082e071]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x2b177081d3ea]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/bin/docking_prepack_protocol.linuxgccrelease() [0x402188]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b1779621555]
/dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/source/bin/docking_prepack_protocol.linuxgccrelease() [0x4022cf]

[END_BACKTRACE]

[FILE]: src/core/pose/util.cc
[LINE]: 1408
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Cannot compute center of mass of zero residues!



[END_MESSAGE]
[END_CRASH_REPORT]

This error seems to indicate zero residues are being selected for one of the two partners, but I'm sure I've provided the correct chains in the flags. Sorry if I've missed something obvious!

Category: 
Post Situation: 
Tue, 2023-02-28 18:17
katherinemccoy