Hi guys, I need a little help.
I run a docking, and I had a great result.
So, I repeat, but change the initial position of one of the proteis.
When I run, this error is showed.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014
protocols.docking.DockingInitialPerturbation: Reading options...
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE
ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 2806
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(print_backtrace()+0x39) [0x7f8c2e2e1299]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libutility.so(utility::exit(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0xd0) [0x7f8c2e2e10d0]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libcore.3.so(core::pose::residue_center_of_mass(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> >)+0x72) [0x7f8c29229632]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols_h.4.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&)+0xbe2) [0x7f8c2f9c1102]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols_h.4.so(protocols::docking::setup_foldtree(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, utility::vector1<int, std::allocator<int> >&)+0x530) [0x7f8c2f9c25c0]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols_h.4.so(protocols::docking::DockingProtocol::finalize_setup(core::pose::Pose&)+0x85) [0x7f8c2f962db5]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols_h.4.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0x116) [0x7f8c2f964326]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(boost::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)+0xe29) [0x7f8c2f26df79]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(boost::shared_ptr<protocols::moves::Mover>)+0x196) [0x7f8c2f270186]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(boost::shared_ptr<protocols::moves::Mover>)+0x4c) [0x7f8c2f23798c]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/bin/docking_protocol.linuxgccrelease() [0x403851]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/bin/docking_protocol.linuxgccrelease() [0x403441]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f8c2d6ac830]
/home/verena/rosetta_bin_linux_2016.11.58563_bundle/main/source/bin/docking_protocol.linuxgccrelease() [0x403529]
protocols.jd2.JobDistributor:
[ERROR] Exception caught by JobDistributor for job S_0001
[ERROR] EXCN_utility_exit has been thrown from: src/core/pose/util.cc line: 2806
ERROR: Cannot compute center of mass of zero residues!
protocols.jd2.JobDistributor: S_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds
caught exception 1 jobs failed; check output for error messages
This is the script used:
-s all_0001Giro_90.pdb \
-nstruct 2 \
-partners P_A \
-dock_pert 3 8 \
-spin false \
-ex1 \
-ex2aro \
-use_input_sc \
-ignore_unrecognized_res \
-ignore_zero_occupancy false \
-out:levels all:warning core.init:info protocols.jd2.JobDistributor:info \
-out:file:silent_struct_type binary \
-out:file:silent all_0001Giro_90.out \
-out:file:fullatom \
-overwrite
Help!!!!
Can you also attach your input PDB? That will help us try to reproduce the issue. You may also be able to solve it on your own: my highest suspicion right now is that either your input file has zero residues in it (who knows what happened!) or chain letter P or A does not have any residues (maybe when you used a program to move one chain, it accidentally relabeled it).
The reason I suspect that is because the error suggests it's trying (and failing, rightfully) to find the center of mass of zero residues. That suggests to me that some component of your input structure -- the most likely components being one of your chains of interest, or the whole darn thing -- is missing quite a number of residues, possibly all of them.
Hi, I have similar questions about, about 'Cannot compute center of mass of zero residues!', Can you help me?
My parameter settings are as follows:
-in:file:s input_files/fgf12-1q1u.pdb
-in:file:native scn1a-7dtd_0001.pdb
-unboundrot input_files/fgf12-1q1u.pdb
-nstruct 2
-partners A_A
-dock_pert 3 8
-ex1
-ex2aro
-ignore_unrecognized_res
-ignore_zero_occupancy false
-out:path:all output_files
-out:suffix _local_dock
Run the command: $ROSETTA/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking
Error message:
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input_files/fgf12-1q1u.pdb
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 138 -1 EDGE 1 139 1 EDGE 1 140 2 EDGE 1 141 3 EDGE 1 142 4
ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1408
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job fgf12-1q1u_local_dock_0002
【The attached file is the PDB of two proteins I use】