Dear Rosetta team,
I wanted to know if cst-design is required for Enzyme Design protocol?
my flags
-s Protein.pdb
-extra_res_fa XOH.params ONN.params
-resfile some.resfile
-enzdes
-cst_design
-cst_opt
-cst_min
-cstfile constraint.cst
-bb_min
-lig_packer_weight 1.8
-design_min_cycles 10
-packing:soft_rep_design
-packing:ex1
-packing:ex2
-out:file:o enz_score.out
-nblist_autoupdate
-unboundrot Protein.pdb
-nstruct 2
-nproc=20
-mute core.io.database core.scoring.NeighborList
-in:file:load_PDB_components
if I use it I am getting error (organometallic protein)
Error: [ ERROR ] Must call shutdown() when finished using job distributor!
caught exception
File: src/numeric/xyzVector.hh:665
Cannot normalize xyzVector of length() zero
Category:
Post Situation:
Using -cst_design should not be required when using the enzyme_design application, but if you don't use it, you're not going to get any mutations. -- You can minimize and rescore without it, but not design.
The "Cannot normalize xyzVector of length() zero" is likely coming from a different thing, possibly related to the metallic portion of your organometallic, but possibly not. It's a bit hard to say with the information provided. Do you have more of the error message? (The backtrace of where the error came from would be helpful. -- Note the line you provided with [ ERROR ] is only a secondary error, and not the primary issue.)
Thanks for the reply.
"You can minimize and rescore without it, but not design" means it wont check for contraints? (I am trying to do near attack geometry check)
backtrace:
===========
protocols.enzdes.EnzdesTaskOperations: Packer Energies between ligand and design residues are upweighted by factor 1.8.
protocols.enzdes.EnzdesFixBBProtocol: starting cst_design, 10 cycles of design/minimization ...
*** Error in `/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/enzyme_design.linuxgccrelease': malloc(): memory corruption: 0x0000000005ea4aa0 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x82c86)[0x7f4536950c86]
/usr/lib64/libc.so.6(__libc_malloc+0x4c)[0x7f453695384c]
/usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x7f4537211ecd]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(_ZNK4core7scoring4elec13FA_ElecEnergy19create_rotamer_trieERKNS_12conformation7ResidueERKNS_4pose4PoseE+0x54f)[0x7f453ba4866f]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(_ZNK4core7scoring4elec13FA_ElecEnergy17setup_for_packingERNS_4pose4PoseERKN7utility7vector1IbSaIbEEESB_+0x140)[0x7f453ba48ac0]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(_ZNK4core7scoring13ScoreFunction17setup_for_packingERNS_4pose4PoseERKN7utility7vector1IbSaIbEEESA_+0x103)[0x7f453ae224f3]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.4.so(_ZN4core4pack19pack_rotamers_setupERNS_4pose4PoseERKNS_7scoring13ScoreFunctionESt10shared_ptrIKNS0_4task10PackerTaskEES8_INS0_11rotamer_set11RotamerSetsEERS8_INS0_17interaction_graph19AnnealableGraphBaseEE+0x74)[0x7f453c92e4d4]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.3.so(_ZN9protocols20minimization_packing17PackRotamersMover5setupERN4core4pose4PoseE+0x121)[0x7f453edf1461]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.3.so(_ZN9protocols20minimization_packing17PackRotamersMover5applyERN4core4pose4PoseE+0x20)[0x7f453edf3390]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.7.so(_ZNK9protocols6enzdes18EnzdesBaseProtocol11enzdes_packERN4core4pose4PoseESt10shared_ptrIKNS2_4pack4task10PackerTaskEES6_IKNS2_7scoring13ScoreFunctionEEmbbb+0x1f6)[0x7f4544f485f6]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.7.so(_ZN9protocols6enzdes19EnzdesFixBBProtocol5applyERN4core4pose4PoseE+0x54f)[0x7f4544f4e32f]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/enzyme_design.linuxgccrelease[0x408063]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f45368f0445]
/home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/enzyme_design.linuxgccrelease[0x409410]
======= Memory map: ========
00400000-00411000 r-xp 00000000 fd:02 5367814745 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/enzyme_design.default.linuxgccrelease
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00612000-00613000 rw-p 00000000 00:00 0
024dd000-1118c000 rw-p 00000000 00:00 0 [heap]
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7f4536cb0000-7f4536eaf000 ---p 00015000 fd:00 67140831 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
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7f45371b1000-7f45371b2000 r--p 00100000 fd:00 67140684 /usr/lib64/libm-2.17.so
7f45371b2000-7f45371b3000 rw-p 00101000 fd:00 67140684 /usr/lib64/libm-2.17.so
7f45371b3000-7f453729c000 r-xp 00000000 fd:00 67141012 /usr/lib64/libstdc++.so.6.0.19
7f453729c000-7f453749b000 ---p 000e9000 fd:00 67141012 /usr/lib64/libstdc++.so.6.0.19
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7f45374a5000-7f45374ba000 rw-p 00000000 00:00 0
7f45374ba000-7f45376eb000 r-xp 00000000 fd:02 2293659440 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default/libxml2.so
7f45376eb000-7f45378eb000 ---p 00231000 fd:02 2293659440 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default/libxml2.so
7f45378eb000-7f45378f3000 r--p 00231000 fd:02 2293659440 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default/libxml2.so
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7f4537cd5000-7f4537dd4000 r-xp 00000000 fd:02 2293659452 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default/libsqlite3.so
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7f4538bac000-7f4538baf000 rw-p 00338000 fd:02 4677399189 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so
7f4538baf000-7f4538bb0000 rw-p 00000000 00:00 0
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7f4538ffa000-7f4539002000 r--p 0024a000 fd:02 4677399191 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libnumeric.so
7f4539002000-7f4539004000 rw-p 00252000 fd:02 4677399191 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libnumeric.so
7f4539004000-7f4539482000 r-xp 00000000 fd:02 4677399192 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libbasic.so
7f4539482000-7f4539681000 ---p 0047e000 fd:02 4677399192 /home/ddas2018/Software/RosettaCommons/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libbasic.so
Aborted (core dumped)