Rotate MOVER

[Anonymous]

I’m trying to use the docking .xml scipts mentioned in the paper “RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite” under the heading “Ligand docking and design”. It is also mentioned in a book chapter “Rosetta Ligand docking with flexible XML protocols.”

I modified it for my purposes (chain name, start from other coordinates). I can produce docked structures, but only if I don’t include the rotate mover by removing it from the low_res_dock mover:

Usually goes right between translate and slide_together.

I’m running this like so:
rosetta_scripts.linuxgccrelease -s input -use_input_sc -nstruct 1 -jd2:ntrials 2 -database /rosetta_database/ -ex1 -ex2 -parser:protocol tmp.xml

I’ve tried to change the Rotate mover to gaussian vs uniform, change the cycles to 0 or 1 and the degrees to small numbers, but I still get the same error.

This is the error:
=======================END MOVER Translate=======================
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol: (0)
}
=======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Rotate=======================
{
protocols.moves.RigidBodyMover: (0) Randomize: Jump (before): RT 0.716929 -0.696282 0.034715 -0.228129 -0.187257 0.955454 -0.658764 -0.692912 -0.293092 21.9288 -3.05299 17.6057
protocols.moves.RigidBodyMover: (0) Randomize: Rot (before): 19.184 -17.992 29.231
protocols.geometry.RB_geometry: (0) random_reorientation_matrix phi: 271.326 psi: 104.019 theta: 131.334
protocols.moves.RigidBodyMover: (0) Randomize: Jump (after): RT -0.600897 -0.552954 -0.577205 -0.689895 0.723473 0.0251353 0.403694 0.413314 -0.816212 23.8292 -2.05493 16.5452
protocols.moves.RigidBodyMover: (0) Randomize: Rot (after): 19.184 -17.992 29.231
protocols.moves.RigidBodyMover: (0) Randomize: —
core.pack.dunbrack: (0) Dunbrack library took 0.02 seconds to load from binary
[sophie:24142] *** Process received signal ***
[sophie:24142] Signal: Segmentation fault (11)
[sophie:24142] Signal code: Address not mapped (1)
[sophie:24142] Failing at address: 0x8
[sophie:24142] [ 0] /lib64/libpthread.so.0 [0x306580eb10]
[sophie:24142] [ 1] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.4.so(_ZNK4core4pack8dunbrack37RotamericSingleResidueDunbrackLibraryILm2EE30chisamples_for_rotamer_and_chiERKNS_8chemical11ResidueTypeERKNS0_4task16ResidueLevelTaskEbmRKNS1_13RotamericDataILm2EEERKN7utility7vector1IdSaIdEEERSJ_RNSH_IiSaIiEEESM_SM_+0xa55) [0x2b8367866bc5]
[sophie:24142] [ 2] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.4.so(_ZNK4core4pack8dunbrack37RotamericSingleResidueDunbrackLibraryILm2EE18enumerate_chi_setsERKNS_8chemical11ResidueTypeERKNS0_4task10PackerTaskEmbRKNS1_13RotamericDataILm2EEERKN7utility7vector1INSH_IdSaIdEEESaISJ_EEERNSH_INSG_7pointer10owning_ptrINS1_6ChiSetEEESaISR_EEE+0xc06) [0x2b836786f336]
[sophie:24142] [ 3] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.4.so(_ZNK4core4pack8dunbrack37RotamericSingleResidueDunbrackLibraryILm2EE19fill_rotamer_vectorERKNS_4pose4PoseERKNS_7scoring13ScoreFunctionERKNS0_4task10PackerTaskEN7utility7pointer10owning_ptrIKNS_5graph5GraphEEENSH_10access_ptrIKNS_8chemical11ResidueTypeEEERKNS_12conformation7ResidueERKNSG_7vector1INSW_IdSaIdEEESaISY_EEEbRNSW_INSI_IST_EESaIS13_EEE+0x3e3) [0x2b8367882bf3]
[sophie:24142] [ 4] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZN9protocols14ligand_docking19rotamers_for_trialsERN4core4pose4PoseEmRN7utility7vector1INS5_7pointer10owning_ptrINS1_12conformation7ResidueEEESaISB_EEE+0x16e) [0x2b836390938e]
[sophie:24142] [ 5] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZN9protocols14ligand_docking27grid_rotamer_trials_atr_repERKN4core4grid8CartGridIiEERNS1_4pose4PoseEm+0x67) [0x2b8363909ab7]
[sophie:24142] [ 6] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZN9protocols14ligand_docking30rb_grid_rotamer_trials_atr_repERKN4core4grid8CartGridIiEERNS1_4pose4PoseEmm+0x65) [0x2b836390a375]
[sophie:24142] [ 7] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZNK9protocols14ligand_docking6Rotate22create_random_rotationERKN7utility7pointer10owning_ptrIN4core4grid8CartGridIiEEEENS4_INS_5rigid14RigidBodyMoverEEEN7numeric9xyzVectorIdEEmmRNS5_4pose4PoseE+0x8b) [0x2b8363983adb]
[sophie:24142] [ 8] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZNK9protocols14ligand_docking6Rotate23create_random_rotationsERKN7utility7pointer10owning_ptrIN4core4grid8CartGridIiEEEENS4_INS_5rigid14RigidBodyMoverEEEmRNS5_4pose4PoseE+0x18e) [0x2b8363985a2e]
[sophie:24142] [ 9] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZN9protocols14ligand_docking6Rotate13rotate_ligandERKN7utility7pointer10owning_ptrIN4core4grid8CartGridIiEEEERNS5_4pose4PoseE+0x8c) [0x2b836398699c]
[sophie:24142] [10] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_h.4.so(_ZN9protocols14ligand_docking6Rotate5applyERN4core4pose4PoseE+0x7a) [0x2b8363986cba]
[sophie:24142] [11] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol23apply_mover_filter_pairERN4core4pose4PoseERKSt4pairIN7utility7pointer10owning_ptrINS_5moves5MoverEEENS9_INS_7filters6FilterEEEE+0xe0) [0x2b8366baba90]
[sophie:24142] [12] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol17sequence_protocolERN4core4pose4PoseEN9__gnu_cxx17__normal_iteratorIPKSt4pairIN7utility7pointer10owning_ptrINS_5moves5MoverEEENSB_INS_7filters6FilterEEEESt6vectorISI_SaISI_EEEE+0x2a) [0x2b8366bb1d6a]
[sophie:24142] [13] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol5applyERN4core4pose4PoseE+0x451) [0x2b8366bb21e1]
[sophie:24142] [14] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol23apply_mover_filter_pairERN4core4pose4PoseERKSt4pairIN7utility7pointer10owning_ptrINS_5moves5MoverEEENS9_INS_7filters6FilterEEEE+0xe0) [0x2b8366baba90]
[sophie:24142] [15] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol17sequence_protocolERN4core4pose4PoseEN9__gnu_cxx17__normal_iteratorIPKSt4pairIN7utility7pointer10owning_ptrINS_5moves5MoverEEENSB_INS_7filters6FilterEEEESt6vectorISI_SaISI_EEEE+0x2a) [0x2b8366bb1d6a]
[sophie:24142] [16] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol5applyERN4core4pose4PoseE+0x451) [0x2b8366bb21e1]
[sophie:24142] [17] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols3jd214JobDistributor7go_mainEN7utility7pointer10owning_ptrINS_5moves5MoverEEE+0xffc) [0x2b8366df110c]
[sophie:24142] [18] /home/gw/rosetta/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols3jd224FileSystemJobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE+0x34) [0x2b8366de3884]
[sophie:24142] [19] /home/gw/rosetta/rosetta3.4/rosetta_source/bin/rosetta_scripts.linuxgccrelease(main+0x11c) [0x40187c]
[sophie:24142] [20] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3064c1d994]
[sophie:24142] [21] /home/gw/rosetta/rosetta3.4/rosetta_source/bin/rosetta_scripts.linuxgccrelease(__gxx_personality_v0+0x101) [0x401579]
[sophie:24142] *** End of error message ***
Segmentation fault

[Anonymous]

I think it is likely this is a version-creep issue: the paper wasn’t using the same version of Rosetta you are. Are you trying 3.3 or 3.4? I’ve brought this to the attention of a ligand docking person for comment.

[Anonymous]

I wrote those papers you cited. If you provide the Rosetta version, the XML file and the PDB input file I could look at them and tell you what the problem is.

[Anonymous]

Here you go – I had to put on a _.txt extension to upload it. I was using version 3.4 and the same errors are produced with version 3.3. Thanks!

[Anonymous]

His XML appears to be dock.txt above? (Also thanks for dropping in!)

[Anonymous]

So I understand the problem and I have a somewhat hacky solution for you. Your ligand is a 2 amino-acid peptide. The rotate code does rotamer sampling for ligands. In this case it is trying to do so for your peptide using Dunbrack rotamer libraries. There is a bug here that will need to be addressed in order for that to happen.

In the meantime you can do the following:
Copy from the Rosetta database the params files for the Leucine and Tyrosine. Change all instances of LEU and TYR to LE1 and TY1 (the exact name here isn’t relevant). Also change the names in the PDB file for chain B. Finally use the flag -in:file:extra_res_fa LE1.params LE2.params. This will allow rotation but removes rotamer sampling.

Alternatively, you can simply learn about Flexible Peptide docking. I don’t know anything about it except that it seems more like what you are looking for…

http://www.rosettacommons.org/manuals/rosetta3.3_user_guide/d7/d14/_flex_pep_dock.html
http://flexpepdock.furmanlab.cs.huji.ac.il/
http://www.ncbi.nlm.nih.gov/pubmed/21622962

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