Error when running enzyme_design tutorial

[Anonymous]

I’m trying to run the enzyme_design tutorial from here:

 

https://www.rosettacommons.org/demos/latest/public/enzyme_design/README

The first 2 stages run fine, but when I run the Design step with the command:

$ROSETTA3/bin/enzyme_design.static.linuxgccrelease @rosetta_inputs/general_design.flags -s rosetta_inputs/UM_1_D41H116K189_1tml_11_mocktim_1.pdb -out:file:o scorefile.txt

The code crashed with the following error:

…

core.pack.task: Packer task: initialize from command line()

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for 1n1

core.pack.task: Packer task: initialize from command line()

core.pack.task: Packer task: initialize from command line()

protocols.enzdes.EnzdesTaskOperations: Choosing the following residues as targets for detecting interface: 287+

protocols.enzdes.EnzdesTaskOperations: Design Interface: detected 0 design-shell residues and 42 repack-shell residues, shell sizes cut1-4 used were 0 0 10 12

protocols.enzdes.EnzdesTaskOperations: Design-shell Residues(pose-numbering):

protocols.enzdes.EnzdesTaskOperations: Repack-shell Residues(pose-numbering): 39+40+41+42+43+44+70+71+72+73+74+75+78+79+85+86+87+113+114+115+116+117+118+121+156+188+189+218+231+232+233+258+259+260+263+264+265+266+270+271+272+287+

protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues:

protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 39, 40, 41, 42, 43, 44, 70, 71, 72, 73, 74, 75, 78, 79, 85, 86, 87, 113, 114, 115, 116, 117, 118, 121, 156, 188, 189, 218, 231, 232, 233, 258, 259, 260, 263, 264, 265, 266, 270, 271, 272, 287,

protocols.enzdes.EnzdesTaskOperations: SetCatalyticResPackBehavior task operation touched the following catalytic residues: 41, 116, 189, 287,

protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization… the backbone is allowed to move at positions: 39, 40, 41, 42, 43, 44, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 84, 85, 86, 87, 88, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 154, 155, 156, 157, 158, 186, 187, 188, 189, 190, 191, 216, 217, 218, 219, 220, 230, 231, 232, 233, 234, 257, 258, 259, 260, 261, 263, 264, 265, 266, 269, 270, 271, 272, 273,

protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 45 -1  EDGE 45 286 -1  EDGE 45 287 1

protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 38 -1  EDGE 38 43 -1  JEDGE 38 45 2 CA CA  END  EDGE 45 44 -1  EDGE 45 69 -1  EDGE 69 73 -1  JEDGE 69 81 3 CA CA  END  EDGE 81 74 -1  EDGE 81 83 -1  EDGE 83 86 -1  JEDGE 83 89 4 CA CA  END  EDGE 89 87 -1  EDGE 89 112 -1  EDGE 112 119 -1  JEDGE 112 123 5 CA CA  END  EDGE 123 120 -1  EDGE 123 153 -1  EDGE 153 155 -1  JEDGE 153 159 6 CA CA  END  EDGE 159 156 -1  EDGE 159 185 -1  EDGE 185 190 -1  JEDGE 185 192 7 CA CA  END  EDGE 192 191 -1  EDGE 192 215 -1  EDGE 215 217 -1  JEDGE 215 221 8 CA CA  END  EDGE 221 218 -1  EDGE 221 229 -1  EDGE 229 232 -1  JEDGE 229 235 9 CA CA  END  EDGE 235 233 -1  EDGE 235 256 -1  EDGE 256 257 -1  JEDGE 256 262 10 CA CA  END  EDGE 262 258 -1  EDGE 262 264 -1  JEDGE 262 267 11 CA CA  END  EDGE 267 265 -1  EDGE 267 268 -1  EDGE 268 270 -1  JEDGE 268 274 12 CA CA  END  EDGE 274 271 -1  EDGE 274 286 -1  EDGE 45 287 1

core.pack.task: Packer task: initialize from command line()

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for 1n1

core.pack.task: Packer task: initialize from command line()

protocols.enzdes.EnzdesTaskOperations: Choosing the following residues as targets for detecting interface: 287+

protocols.enzdes.EnzdesTaskOperations: Design Interface: detected 0 design-shell residues and 37 repack-shell residues, shell sizes cut1-4 used were 0 0 10 12

protocols.enzdes.EnzdesTaskOperations: Design-shell Residues(pose-numbering):

protocols.enzdes.EnzdesTaskOperations: Repack-shell Residues(pose-numbering): 40+41+42+43+44+71+72+73+74+78+79+84+85+86+87+113+114+115+116+117+118+156+188+189+232+233+258+259+260+263+264+265+266+270+271+272+287+

protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues:

protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 40, 41, 42, 43, 44, 71, 72, 73, 74, 78, 79, 84, 85, 86, 87, 113, 114, 115, 116, 117, 118, 156, 188, 189, 232, 233, 258, 259, 260, 263, 264, 265, 266, 270, 271, 272, 287,

protocols.enzdes.EnzdesTaskOperations: SetCatalyticResPackBehavior task operation touched the following catalytic residues: 41, 116, 189, 287,

protocols.enzdes.EnzdesFixBBProtocol: Starting after design unconstrained repack/minimization…

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for 1n1

core.pack.pack_rotamers: built 1857 rotamers at 37 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 754383 bytes

protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization… the backbone is allowed to move at positions: 40, 41, 42, 43, 44, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 85, 86, 87, 113, 114, 115, 116, 117, 118, 154, 155, 156, 157, 158, 186, 187, 188, 189, 190, 191, 230, 231, 232, 233, 234, 235, 257, 258, 259, 260, 261, 263, 264, 265, 266, 269, 270, 271, 272, 273,

protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 75 -1  EDGE 75 286 -1  EDGE 75 287 1

protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 39 -1  EDGE 39 40 -1  JEDGE 39 45 2 CA CA  END  EDGE 45 41 -1  EDGE 45 70 -1  EDGE 70 71 -1  JEDGE 70 75 3 CA CA  END  EDGE 75 72 -1  EDGE 75 80 -1  JEDGE 75 82 4 CA CA  END  EDGE 82 81 -1  EDGE 82 83 -1  EDGE 83 84 -1  JEDGE 83 88 5 CA CA  END  EDGE 88 85 -1  EDGE 88 112 -1  EDGE 112 113 -1  JEDGE 112 119 6 CA CA  END  EDGE 119 114 -1  EDGE 119 153 -1  EDGE 153 156 -1  JEDGE 153 159 7 CA CA  END  EDGE 159 157 -1  EDGE 159 185 -1  EDGE 185 188 -1  JEDGE 185 192 8 CA CA  END  EDGE 192 189 -1  EDGE 192 229 -1  EDGE 229 234 -1  JEDGE 229 236 9 CA CA  END  EDGE 236 235 -1  EDGE 236 256 -1  EDGE 256 257 -1  JEDGE 256 262 10 CA CA  END  EDGE 262 258 -1  EDGE 262 263 -1  JEDGE 262 267 11 CA CA  END  EDGE 267 264 -1  EDGE 267 268 -1  EDGE 268 271 -1  JEDGE 268 274 12 CA CA  END  EDGE 274 272 -1  EDGE 274 286 -1  EDGE 75 287 1

core.pack.task: Packer task: initialize from command line()

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for 1n1

protocols.enzdes.EnzdesFixBBProtocol: Finished after design unconstrained repack/minimization…

basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/average_hASA_by_res_and_neighbor.txt

basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/surface_score.txt

basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/hpatch_score.txt

terminate called after throwing an instance of ‘std::regex_error’

  what():  regex_error

Aborted (core dumped)

 

 

I’ve not altered the files in any way.

I’m running this on Ubuntu 16.04 with rosetta_bin_linux_2017.08.59291_bundle

Any suggestions as to what to do would be appreciated.

 

[Anonymous]

Which compiler did you use to compile? There are issues with earlier versions of GCC (e.g. 4. and regex support. (This will also extend to Linux Clang installations which use GCC 4.8 standard libraries.)

I’d recommend recompiling with GCC 5.2 or later, or at the very least GCC 4.9 or later.

[Anonymous]

After a bit of rooting around with gdb, i’ve isolated the problem to where it tries to compare things to the native pdb.

Removing the “-compare_native rosetta_inputs/native_pdbs” flag  from the general_design.flags  allowed this stage to complete.

I’m posting this in case anyone else encounters this problem, although the original issue is still there.

[Anonymous]

Alternatively, you might want to try going back to Rosetta 3.7 (versus 3., which doesn’t use std::regex in this location.

[Anonymous]

Thanks for the reply.

 

I didn’t compile as I downloaded the pre-compiled bundle: rosetta_bin_linux_2017.08.59291_bundle

 

I’ll recompile if I need the “-compare_native” functionality, but I don’t think I need this and it’s working fine otherwise now.

[Author]

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