Problem with symmetric docking

[Anonymous]

Hello everyone,
I’m trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown
core.init: command: /house/homedirs/s/saxen/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1610051349 seed_offset=0 real_seed=-1610051349
core.init.random: RandomGenerator:init: Normal mode, seed=-1610051349 RG_type=mt19937
core.io.database: Database file opened: ../rosetta_database/env_log.txt
core.io.database: Database file opened: ../rosetta_database/cbeta_den.txt
core.io.database: Database file opened: ../rosetta_database/pair_log.txt
core.io.database: Database file opened: ../rosetta_database/cenpack_log.txt
core.io.database: Database file opened: ../rosetta_database/interchain_env_log.txt
core.io.database: Database file opened: ../rosetta_database/interchain_pair_log.txt
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
core.io.database: Database file opened: ../rosetta_database/pdb_pair_stats_fine
core.io.database: Database file opened: ../rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
core.io.database: Database file opened: ../rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
core.io.database: Database file opened: ../rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
core.io.database: Database file opened: ../rosetta_database/P_AA
core.io.database: Database file opened: ../rosetta_database/P_AA_n
core.io.database: Database file opened: ../rosetta_database/P_AA_pp
protocols.docking.DockingInitialPerturbation: Reading options...
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushing INPUT.pdb nstruct index 1
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 89 in file INPUT.pdb. Best match rsd_type: ILE
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 90 in file INPUT.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 180 in file INPUT.pdb. Best match rsd_type: PHE
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 181 in file INPUT.pdb. Best match rsd_type: GLN
core.pack.task: Packer task: initialize from command line()
core.io.pdb.file_data: [ WARNING ] can't find atom for res 89 atom OXT (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 90 atom 1H (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 90 atom 2H (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 90 atom 3H (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 180 atom OXT (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 181 atom 1H (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 181 atom 2H (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can't find atom for res 181 atom 3H (trying to set temp)
protocols.jd2.PDBJobInputter: filling pose from PDB INPUT.pdb
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 269 -1
protocols.docking.DockingProtocol:

ERROR: cutpoint
ERROR:: Exit from: src/protocols/docking/util.cc line: 91

I can do normal docking just fine. Any ideas as to why this might be failing? Thanks!

[Anonymous]

When you say you can do normal docking fine, do you mean on the exact same PDB? The cutpoint complaint causes me to guess that it is reading the PDB in as one chain. (Of course, you have two OXT warnings, which goes against that guess.) Are the chains lettered differently, preferably with a TER card between them?

[Anonymous]

I went back and checked, and I was mistaken. Apparently this structure also fails normal docking, though I don’t know why. This structure is actually a trimer of trimers, so what I had done was renumber the three subunits of the first trimer so that there was no overlap in numbers and then concatenate them into one chain. I then tried to use symmetry dock on this chain to generate the second trimer, and that’s where it failed. I suspect something in my method for concatenating the three proteins is wrong.

[Anonymous]

Post the PDB (as attachment) and I’ll see if I can spot anything. Also, I wasn’t quite clear on what you did – you converted a trimer into a pretend-monomer (makes sense), then fed what to Rosetta? That pseudomonomer, two of them, three of them?

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