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Fold tree error

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Fold tree error
#1
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I am doing protein-protein docking and I am getting this error. My pdb file is prepared according to rosetta instructions. I am not able to understand the cause of the error. Can anyone help me with this error.
I am using rosetta3.1.

####################################ERROR###############################################
core.init: command: docking_protocol.linuxgccrelease @flags -database /share/apps/rosetta3.1/rosetta_database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1512441785 seed_offset=0 real_seed=1512441785
core.init.random: RandomGenerator:init: Normal mode, seed=1512441785 RG_type=mt19937
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/env_log.txt
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/cbeta_den.txt
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/pair_log.txt
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/cenpack_log.txt
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/interchain_env_log.txt
core.io.database: Database file opened: /share/apps/rosetta3.1/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: /share/apps/rosetta3.1/rosetta_database/pdb_pair_stats_fine
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/P_AA
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/P_AA_n
core.io.database: Database file opened: /share/apps/rosetta3.1/rosetta_database/P_AA_pp
core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
core.init: command: docking_protocol.linuxgccrelease @flags -database /share/apps/rosetta3.1/rosetta_database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1527558935 seed_offset=0 real_seed=1527558935
core.init.random: RandomGenerator:init: Normal mode, seed=1527558935 RG_type=mt19937
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 input/3116.pdb 1
protocols.jobdist.main: Starting 3116_0001 ...
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA_p:CtermProteinFull 201
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA_p:CtermProteinFull 397
core.pack.task: Packer task: initialize from command line()
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA_p:CtermProteinFull 201
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA_p:CtermProteinFull 397
core.pack.task: Packer task: initialize from command line()
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 201 -1 EDGE 1 202 1 EDGE 202 397 -1 EDGE 1 398 2 EDGE 398 653 -1
protocols.docking.DockingProtocol:
core.kinematics.FoldTree: FoldTree::reorder( 202 ) failed, new/old edge_list_ size mismatch
core.kinematics.FoldTree: 7 1
core.kinematics.FoldTree: FOLD_TREE EDGE 202 397 -1 EDGE 1 398 2 EDGE 1 137 -1 EDGE 137 201 -1 EDGE 398 576 -1 EDGE 576 653 -1 EDGE 137 576 1
core.kinematics.FoldTree: FoldTree::reorder( 202 ) failed, new/old edge_list_ size mismatch
core.kinematics.FoldTree: 7 1
core.kinematics.FoldTree: FOLD_TREE EDGE 202 397 -1 EDGE 137 576 1 EDGE 1 137 -1 EDGE 137 201 -1 EDGE 398 576 -1 EDGE 576 653 -1 EDGE 137 576 2
core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch
core.kinematics.FoldTree: 7 5
core.kinematics.FoldTree: FOLD_TREE EDGE 202 397 -1 EDGE 137 576 1 EDGE 1 137 -1 EDGE 137 201 -1 EDGE 398 576 -1 EDGE 576 653 -1 EDGE 137 576 2
core.kinematics.FoldTree: bad fold tree at edge 137--576 !
core.kinematics.FoldTree: FOLD_TREE EDGE 202 397 -1 EDGE 137 576 1 EDGE 1 137 -1 EDGE 137 201 -1 EDGE 398 576 -1 EDGE 576 653 -1 EDGE 137 576 2
core.kinematics.FoldTree:
core.kinematics.FoldTree: bad fold tree at edge 137--576 !
core.kinematics.FoldTree: FOLD_TREE EDGE 202 397 -1 EDGE 137 576 1 EDGE 1 137 -1 EDGE 137 201 -1 EDGE 398 576 -1 EDGE 576 653 -1 EDGE 137 576 2
core.kinematics.FoldTree:

ERROR: f.check_fold_tree()
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 327

Tue, 2010-05-18 07:43
mansi
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It looks like it may be angry because you have too many chains in the starting pdb?

Wed, 2010-05-19 13:22
smlewis
(Reply to #3)
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> It looks like it may be angry because you have too many chains in the starting pdb?

Thanks for yuour reply.
Yes I have two chains in protein 1 and one in protein 2.Both the proteins are combined in single pdb and the pdb is refined according to rosetta manul.
What can I do to solve the error?

Tue, 2010-05-25 01:24
mansi