Is CST_Design required for enzdes protocol?

[Anonymous]

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

[Anonymous]

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.)

 

[Anonymous]

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

00610000-00611000 r–p 00010000 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

00611000-00612000 rw-p 00011000 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

00612000-00613000 rw-p 00000000 00:00 0

024dd000-1118c000 rw-p 00000000 00:00 0                                  [heap]

7f4530000000-7f4530021000 rw-p 00000000 00:00 0

7f4530021000-7f4534000000 —p 00000000 00:00 0

7f4534619000-7f4534ea7000 rw-p 00000000 00:00 0

7f4535733000-7f45366ca000 rw-p 00000000 00:00 0

7f45366ca000-7f45366cc000 r-xp 00000000 fd:00 67140682                   /usr/lib64/libdl-2.17.so

7f45366cc000-7f45368cc000 —p 00002000 fd:00 67140682                   /usr/lib64/libdl-2.17.so

7f45368cc000-7f45368cd000 r–p 00002000 fd:00 67140682                   /usr/lib64/libdl-2.17.so

7f45368cd000-7f45368ce000 rw-p 00003000 fd:00 67140682                   /usr/lib64/libdl-2.17.so

7f45368ce000-7f4536a91000 r-xp 00000000 fd:00 67140676                   /usr/lib64/libc-2.17.so

7f4536a91000-7f4536c90000 —p 001c3000 fd:00 67140676                   /usr/lib64/libc-2.17.so

7f4536c90000-7f4536c94000 r–p 001c2000 fd:00 67140676                   /usr/lib64/libc-2.17.so

7f4536c94000-7f4536c96000 rw-p 001c6000 fd:00 67140676                   /usr/lib64/libc-2.17.so

7f4536c96000-7f4536c9b000 rw-p 00000000 00:00 0

7f4536c9b000-7f4536cb0000 r-xp 00000000 fd:00 67140831                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1

7f4536cb0000-7f4536eaf000 —p 00015000 fd:00 67140831                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1

7f4536eaf000-7f4536eb0000 r–p 00014000 fd:00 67140831                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1

7f4536eb0000-7f4536eb1000 rw-p 00015000 fd:00 67140831                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1

7f4536eb1000-7f4536fb2000 r-xp 00000000 fd:00 67140684                   /usr/lib64/libm-2.17.so

7f4536fb2000-7f45371b1000 —p 00101000 fd:00 67140684                   /usr/lib64/libm-2.17.so

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

7f453749b000-7f45374a3000 r–p 000e8000 fd:00 67141012                   /usr/lib64/libstdc++.so.6.0.19

7f45374a3000-7f45374a5000 rw-p 000f0000 fd:00 67141012                   /usr/lib64/libstdc++.so.6.0.19

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

7f45378f3000-7f45378f7000 rw-p 00239000 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

7f45378f7000-7f4537909000 rw-p 00000000 00:00 0

7f4537909000-7f4537ad1000 r-xp 00000000 fd:02 2293659426                 /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/libcifparse.so

7f4537ad1000-7f4537cd0000 —p 001c8000 fd:02 2293659426                 /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/libcifparse.so

7f4537cd0000-7f4537cd2000 r–p 001c7000 fd:02 2293659426                 /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/libcifparse.so

7f4537cd2000-7f4537cd5000 rw-p 001c9000 fd:02 2293659426                 /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/libcifparse.so

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

7f4537dd4000-7f4537fd3000 —p 000ff000 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

7f4537fd3000-7f4537fd5000 r–p 000fe000 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

7f4537fd5000-7f4537fd7000 rw-p 00100000 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

7f4537fd7000-7f4537fd8000 rw-p 00000000 00:00 0

7f4537fd8000-7f4538017000 r-xp 00000000 fd:02 2293659453                 /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/libcppdb.so

7f4538017000-7f4538217000 —p 0003f000 fd:02 2293659453                 /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/libcppdb.so

7f4538217000-7f4538218000 r–p 0003f000 fd:02 2293659453                 /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/libcppdb.so

7f4538218000-7f4538219000 rw-p 00040000 fd:02 2293659453                 /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/libcppdb.so

7f4538219000-7f453822e000 r-xp 00000000 fd:00 67140833                   /usr/lib64/libz.so.1.2.7

7f453822e000-7f453842d000 —p 00015000 fd:00 67140833                   /usr/lib64/libz.so.1.2.7

7f453842d000-7f453842e000 r–p 00014000 fd:00 67140833                   /usr/lib64/libz.so.1.2.7

7f453842e000-7f453842f000 rw-p 00015000 fd:00 67140833                   /usr/lib64/libz.so.1.2.7

7f453842f000-7f4538472000 r-xp 00000000 fd:02 4677399188                 /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/libObjexxFCL.so

7f4538472000-7f4538672000 —p 00043000 fd:02 4677399188                 /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/libObjexxFCL.so

7f4538672000-7f4538673000 r–p 00043000 fd:02 4677399188                 /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/libObjexxFCL.so

7f4538673000-7f4538674000 rw-p 00044000 fd:02 4677399188                 /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/libObjexxFCL.so

7f4538674000-7f45389a0000 r-xp 00000000 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

7f45389a0000-7f4538b9f000 —p 0032c000 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

7f4538b9f000-7f4538bac000 r–p 0032b000 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

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

7f4538bb0000-7f4538dfb000 r-xp 00000000 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

7f4538dfb000-7f4538ffa000 —p 0024b000 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

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)

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