Error running snugdock

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    • March 14, 2017 at 5:00 pm #2618
      Anonymous

        Hi,

        I’m following the antibody modeling protocol recently published in Nature Protocols “Modeling and docking of antibody structures

        with Rosetta”.  I run into an error when running snugdock with ensembles.  I get a segfault (last couple lines posted) with no additional info.  However, if I don’t specify to run with ensembles, the snugdock run proceeds to completion.  I’m using rosetta3.8.

         ~/rosetta/bin/snugdock.linuxgccrelease @snugdock.flags

        tail of output:

        protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

        protocols.docking.DockingLowRes: /// Ensemble 1: on                                                           ///

        protocols.docking.DockingLowRes: /// Ensemble 2: on                                                           ///

        protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::

        Segmentation fault (core dumped)

         

        Here’s my flags file:

        -s complex.prepack.pdb

        -out:file:scorefile score_out_snugdockC.sc

        -out:path:pdb snugdock_models

        -antibody:auto_generate_kink_constraint

        -antibody:all_atom_mode_kink_constraint

        # Docking

        #-partners LH_ABD   # Tried with and without this 

        -ensemble1 ensemble_antibody.list   # removing these two lines will make it work

        -ensemble2 ensemble_antigen.list

        # rotamer settings

        #-ex1

        #-ex2aro

        -detect_disulf false

        -nstruct 1

        I’ve attached my full log file.  My ensemble lists contain full paths to all structures (indeed, they seem to be correctly read based on the log file).

        Any ideas what could be going wrong?

         

        Thanks!

         

      • March 14, 2017 at 5:27 pm #12225
        Anonymous

          Just to add a little more information to the above post.  After getting the error above, I have tried to make sure that there are no errors in the ensemble.  One thing I have tried is to take my input pdb (complex.prepack.pdb) and extract the antibody (using a text editor) and the antigen, and stored them in separate files (mab1.pdb, mab2.pdb in my antibody ensemble and ag1.pdb and ag2.pdb in my antigen ensemble).  Here mab1.pdb, mab2.pdb, and the antibody portion of my input structure are all identical, and ag1.pdb, ag2.pdb, and the antigen portion of my input structure are all identical.  However, I still get the segfault.

        • March 14, 2017 at 5:27 pm #12746
          Anonymous

            Just to add a little more information to the above post.  After getting the error above, I have tried to make sure that there are no errors in the ensemble.  One thing I have tried is to take my input pdb (complex.prepack.pdb) and extract the antibody (using a text editor) and the antigen, and stored them in separate files (mab1.pdb, mab2.pdb in my antibody ensemble and ag1.pdb and ag2.pdb in my antigen ensemble).  Here mab1.pdb, mab2.pdb, and the antibody portion of my input structure are all identical, and ag1.pdb, ag2.pdb, and the antigen portion of my input structure are all identical.  However, I still get the segfault.

          • March 14, 2017 at 5:27 pm #13267
            Anonymous

              Just to add a little more information to the above post.  After getting the error above, I have tried to make sure that there are no errors in the ensemble.  One thing I have tried is to take my input pdb (complex.prepack.pdb) and extract the antibody (using a text editor) and the antigen, and stored them in separate files (mab1.pdb, mab2.pdb in my antibody ensemble and ag1.pdb and ag2.pdb in my antigen ensemble).  Here mab1.pdb, mab2.pdb, and the antibody portion of my input structure are all identical, and ag1.pdb, ag2.pdb, and the antigen portion of my input structure are all identical.  However, I still get the segfault.

            • March 14, 2017 at 6:27 pm #12226
              Anonymous

                Hmmm… First, the -partners flag is necessary. Second, the chain order specified by the partners flag should be consistent with the chain order in the input (specified by -s) and in the ensemble pdbs. However, it seems like you’ve tested for these issues. Could you possible compile rosetta in debug mode (mode=debug, rather than mode=release)? Then run ~/rosetta/bin/snugdock.linuxgccdebug.

              • March 14, 2017 at 6:27 pm #12747
                Anonymous

                  Hmmm… First, the -partners flag is necessary. Second, the chain order specified by the partners flag should be consistent with the chain order in the input (specified by -s) and in the ensemble pdbs. However, it seems like you’ve tested for these issues. Could you possible compile rosetta in debug mode (mode=debug, rather than mode=release)? Then run ~/rosetta/bin/snugdock.linuxgccdebug.

                • March 14, 2017 at 6:27 pm #13268
                  Anonymous

                    Hmmm… First, the -partners flag is necessary. Second, the chain order specified by the partners flag should be consistent with the chain order in the input (specified by -s) and in the ensemble pdbs. However, it seems like you’ve tested for these issues. Could you possible compile rosetta in debug mode (mode=debug, rather than mode=release)? Then run ~/rosetta/bin/snugdock.linuxgccdebug.

                  • March 16, 2017 at 3:08 pm #12234
                    Anonymous

                      Would it be possible to get a couple input structures from the Nature Protocols paper  (maybe from one of the authors) so that I can ensure those structures work with my compiled version of ensemble snugdock?  If I can show those structures work, then I can figure out the differences between my input structure and the ones used in the paper.

                       

                      Thanks!

                    • March 16, 2017 at 3:08 pm #12755
                      Anonymous

                        Would it be possible to get a couple input structures from the Nature Protocols paper  (maybe from one of the authors) so that I can ensure those structures work with my compiled version of ensemble snugdock?  If I can show those structures work, then I can figure out the differences between my input structure and the ones used in the paper.

                         

                        Thanks!

                      • March 16, 2017 at 3:08 pm #13276
                        Anonymous

                          Would it be possible to get a couple input structures from the Nature Protocols paper  (maybe from one of the authors) so that I can ensure those structures work with my compiled version of ensemble snugdock?  If I can show those structures work, then I can figure out the differences between my input structure and the ones used in the paper.

                           

                          Thanks!

                        • March 29, 2017 at 1:40 pm #12246
                          Anonymous

                            Just wanted to check in again and see if anyone has any ideas how to fix this issue.  Based on my naive interpretation of the output from the debug build, I’m not sure whether the problem is with my input structures.  However, if there isn’t a bug, does anyone have a working pdb example that I can use to see how my input structures differ?

                             

                            Thanks.

                          • March 29, 2017 at 1:40 pm #12767
                            Anonymous

                              Just wanted to check in again and see if anyone has any ideas how to fix this issue.  Based on my naive interpretation of the output from the debug build, I’m not sure whether the problem is with my input structures.  However, if there isn’t a bug, does anyone have a working pdb example that I can use to see how my input structures differ?

                               

                              Thanks.

                            • March 29, 2017 at 1:40 pm #13288
                              Anonymous

                                Just wanted to check in again and see if anyone has any ideas how to fix this issue.  Based on my naive interpretation of the output from the debug build, I’m not sure whether the problem is with my input structures.  However, if there isn’t a bug, does anyone have a working pdb example that I can use to see how my input structures differ?

                                 

                                Thanks.

                              • March 14, 2017 at 8:53 pm #12228
                                Anonymous

                                  Thanks for the prompt reply.  I compiled rosetta in debug mode and reran.  Here’s the tail of the output:

                                   

                                  protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

                                  protocols.docking.DockingLowRes: /// Ensemble 1: on                                                           ///

                                  protocols.docking.DockingLowRes: /// Ensemble 2: on                                                           ///

                                  protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::

                                  protocols.docking.ConformerSwitchMover: Switching partner with conformer: 1

                                  /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace(char const*)+0x3e) [0x405ceb]

                                  /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace_NR(char const*)+0x18) [0x405e46]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(utility::vectorL<1l, double, std::allocator<double> >::operator[](unsigned long)+0x5e) [0x2aaaac2877de]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long)+0x2a) [0x2aaab0e3d5ea]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::ConformerSwitchMover::apply(core::pose::Pose&)+0x37e) [0x2aaab0e3b666]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::SequenceMover::apply(core::pose::Pose&)+0x2b8) [0x2aaab7b780bc]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::TrialMover::apply(core::pose::Pose&)+0xd3) [0x2aaab7bb9717]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::RepeatMover::apply(core::pose::Pose&)+0x3f) [0x2aaab7ba7b65]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::rigid_body_trial(core::pose::Pose&)+0x1ca) [0x2aaab0e72a0c]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::apply(core::pose::Pose&)+0x139) [0x2aaab0e726d5]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0x5f1) [0x2aaab0e81cbf]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(protocols::antibody::snugdock::SnugDockProtocol::apply(core::pose::Pose&)+0x2f0) [0x2aaaac53803a]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/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)+0xf21) [0x2aaab7f10553]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xb4) [0x2aaab7f0ea0a]

                                  /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x46) [0x2aaab7ee7766]

                                  /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404c82]

                                  /lib64/libc.so.6(__libc_start_main+0xfd) [0x2aaac18ead5d]

                                  /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404729]

                                  snugdock.linuxgccdebug: src/utility/backtrace.hh:162: bool print_backtrace_NR(const char*): Assertion `false’ failed.

                                  Got some signal… It is:6

                                  Process was aborted!

                                   

                                  Thanks!

                                • March 14, 2017 at 8:53 pm #12749
                                  Anonymous

                                    Thanks for the prompt reply.  I compiled rosetta in debug mode and reran.  Here’s the tail of the output:

                                     

                                    protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

                                    protocols.docking.DockingLowRes: /// Ensemble 1: on                                                           ///

                                    protocols.docking.DockingLowRes: /// Ensemble 2: on                                                           ///

                                    protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::

                                    protocols.docking.ConformerSwitchMover: Switching partner with conformer: 1

                                    /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace(char const*)+0x3e) [0x405ceb]

                                    /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace_NR(char const*)+0x18) [0x405e46]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(utility::vectorL<1l, double, std::allocator<double> >::operator[](unsigned long)+0x5e) [0x2aaaac2877de]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long)+0x2a) [0x2aaab0e3d5ea]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::ConformerSwitchMover::apply(core::pose::Pose&)+0x37e) [0x2aaab0e3b666]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::SequenceMover::apply(core::pose::Pose&)+0x2b8) [0x2aaab7b780bc]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::TrialMover::apply(core::pose::Pose&)+0xd3) [0x2aaab7bb9717]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::RepeatMover::apply(core::pose::Pose&)+0x3f) [0x2aaab7ba7b65]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::rigid_body_trial(core::pose::Pose&)+0x1ca) [0x2aaab0e72a0c]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::apply(core::pose::Pose&)+0x139) [0x2aaab0e726d5]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0x5f1) [0x2aaab0e81cbf]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(protocols::antibody::snugdock::SnugDockProtocol::apply(core::pose::Pose&)+0x2f0) [0x2aaaac53803a]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/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)+0xf21) [0x2aaab7f10553]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xb4) [0x2aaab7f0ea0a]

                                    /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x46) [0x2aaab7ee7766]

                                    /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404c82]

                                    /lib64/libc.so.6(__libc_start_main+0xfd) [0x2aaac18ead5d]

                                    /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404729]

                                    snugdock.linuxgccdebug: src/utility/backtrace.hh:162: bool print_backtrace_NR(const char*): Assertion `false’ failed.

                                    Got some signal… It is:6

                                    Process was aborted!

                                     

                                    Thanks!

                                  • March 14, 2017 at 8:53 pm #13270
                                    Anonymous

                                      Thanks for the prompt reply.  I compiled rosetta in debug mode and reran.  Here’s the tail of the output:

                                       

                                      protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

                                      protocols.docking.DockingLowRes: /// Ensemble 1: on                                                           ///

                                      protocols.docking.DockingLowRes: /// Ensemble 2: on                                                           ///

                                      protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::

                                      protocols.docking.ConformerSwitchMover: Switching partner with conformer: 1

                                      /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace(char const*)+0x3e) [0x405ceb]

                                      /home/amwoll/rosetta/bin/snugdock.linuxgccdebug(print_backtrace_NR(char const*)+0x18) [0x405e46]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(utility::vectorL<1l, double, std::allocator<double> >::operator[](unsigned long)+0x5e) [0x2aaaac2877de]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long)+0x2a) [0x2aaab0e3d5ea]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::ConformerSwitchMover::apply(core::pose::Pose&)+0x37e) [0x2aaab0e3b666]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::SequenceMover::apply(core::pose::Pose&)+0x2b8) [0x2aaab7b780bc]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::TrialMover::apply(core::pose::Pose&)+0xd3) [0x2aaab7bb9717]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::moves::RepeatMover::apply(core::pose::Pose&)+0x3f) [0x2aaab7ba7b65]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::rigid_body_trial(core::pose::Pose&)+0x1ca) [0x2aaab0e72a0c]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingLowRes::apply(core::pose::Pose&)+0x139) [0x2aaab0e726d5]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols_h.4.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0x5f1) [0x2aaab0e81cbf]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.6.so(protocols::antibody::snugdock::SnugDockProtocol::apply(core::pose::Pose&)+0x2f0) [0x2aaaac53803a]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/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)+0xf21) [0x2aaab7f10553]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xb4) [0x2aaab7f0ea0a]

                                      /home/amwoll/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/build/src/debug/linux/2.6/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x46) [0x2aaab7ee7766]

                                      /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404c82]

                                      /lib64/libc.so.6(__libc_start_main+0xfd) [0x2aaac18ead5d]

                                      /home/amwoll/rosetta/bin/snugdock.linuxgccdebug() [0x404729]

                                      snugdock.linuxgccdebug: src/utility/backtrace.hh:162: bool print_backtrace_NR(const char*): Assertion `false’ failed.

                                      Got some signal… It is:6

                                      Process was aborted!

                                       

                                      Thanks!

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