Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:
remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc
model3.pdb covers the range: 1-393
model4 covers the range: 290 - 393
Where the blueprint has the following general format:
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<All preceding residues unchanged>
280 R .
281 D .
282 R .
283 R .
284 T .
285 E .
286 E L PIKAA E
287 E L PIKAA E
288 N L PIKAA N
289 L L PIKAA L
0 x I NATRO
0 x I NATRO
0 x I NATRO
0 x I NATRO
<The remaining residues treated as insertion and followed by EOF>
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However when it is run the following error occurs:
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protocols.forge.remodel.RemodelWorkingSet: segment contains insertion, skip normal SegmentRebuild instructions, use SegmentInsert instructions instead
protocols.forge.remodel.RemodelWorkingSet: beforeInsert: LLLL
protocols.forge.remodel.RemodelWorkingSet: afterInsert:
protocols.forge.remodel.RemodelWorkingSet: insert_SS_string: LLLL^
core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!
core.conformation.Residue: --> generating it using idealized coordinates.
ERROR: seqpos >= 1
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 379
/mnt/Programs/Rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libutility.so(print_backtrace()+0x23) [0x7f3b935fc093]
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I have looked for this error and it seems to pop us in the protein design segment, but I am not quite sure where or how to correct it. Any thoughts would be welcome.
| Attachment | Size |
|---|---|
 model3.blueprint.txt | 3.4 KB |
 model3.pdb | 473.58 KB |
| model4.pdb | 130.4 KB |
Hi I have figured part of the work-around for the above problems. Now it crashes in the process of manual design. If the inserted region is on the n-terminus of the full model it passes through the first stages of the loop modeling before crashing.
remodel.linuxgccrelease -s model3.pdb -remodel:domainFusion:insert_segment_from_pdb model4-nterm.pdb -remodel:blueprint model3-nterm.blueprint -use_input_sc -save_top 1 -overwrite -out:file:scorefile model3-nterm.sc
model3.pdb covers the range: 1-393
model4-nterm covers the range: 1-293
Where the blueprint has the following general format:
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<All preceding residues inserted>
0 x I NATRO
0 x I NATRO
0 x I NATRO
0 x I NATRO
294 E L PIKAA E
295 P L PIKAA P
296 H L PIKAA H
297 H L PIKAA H
< All succeeding residues unchanged and followed by EOF>
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Incomplete: Ends after initial moving and scoring
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protocols.forge.remodel.RemodelLoopMover: ** randomize_stage
protocols.forge.remodel.RemodelLoopMover: * closure_attempt 1
protocols.forge.remodel.RemodelLoopMover: ** simultaneous_stage
protocols.forge.remodel.RemodelLoopMover: n_loops = 1
protocols.forge.remodel.RemodelLoopMover:
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Scores Weight Raw Score Wghtd.Score
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vdw 1.000 5.369 5.369
hbond_sr_bb 1.000 -136.160 -136.160
hbond_lr_bb 1.000 -3.063 -3.063
rama 0.100 -24.283 -2.428
rg 1.000 39.446 39.446
---------------------------------------------------
Total weighted score: -96.836
protocols.moves.MonteCarlo: MC: 2 -66.7454 -96.8365 -66.7454 -96.8365 0 0 0 rejected
protocols.moves.TrialCounter: simul_frag trials= 23760; accepts= 0.1666; energy_drop/trial= -0.07959
protocols.forge.remodel.RemodelLoopMover: ** independent_stage
protocols.forge.remodel.RemodelLoopMover: n_loops = 1
protocols.forge.remodel.RemodelLoopMover:
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Scores Weight Raw Score Wghtd.Score
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vdw 1.000 4.618 4.618
hbond_sr_bb 1.000 -145.384 -145.384
hbond_lr_bb 1.000 -2.082 -2.082
rama 0.100 -41.183 -4.118
rg 1.000 41.436 41.436
---------------------------------------------------
Total weighted score: -105.531
protocols.moves.MonteCarlo: MC: 2 -86.9267 -105.531 -86.9267 -105.531 0 0 0 rejected
protocols.moves.TrialCounter: frag trials= 95040; accepts= 0.1638; energy_drop/trial= 0.00010
protocols.forge.remodel.RemodelLoopMover: ** boost_closure_stage
protocols.forge.remodel.RemodelLoopMover: n_loops = 0
protocols.forge.remodel.RemodelLoopMover: no loops to work on with boost_closure. returning.
protocols.forge.remodel.RemodelLoopMover: * 1 / 1 closed / attempts
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 0 rotamers at 0 positions.
core.pack.pack_rotamers: IG: 472 bytes
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 0 rotamers at 0 positions.
core.pack.pack_rotamers: IG: 472 bytes
protocols.forge.remodel.RemodelMover: centroid_build(): variable length build succeeded.
protocols.forge.remodel.RemodelMover: apply(): calling RemodelDesignMover apply function.
protocols.forge.remodel.RemodelDesignMover: Design Mover state: stage
protocols.forge.remodel.RemodelDesignMover: MODE 4: Manual DESIGN REMODEL
core.pack.task: Packer task: initialize from command line()
core.pack.task.ResfileReader: On line 3, the pose does not have residue with chain= , PDBnum=1.
ERROR:: Exit from: src/core/pack/task/ResfileReader.cc line: 1520
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