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Fusing C-terminal or N-terminal segments onto proteins using Remodel

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Fusing C-terminal or N-terminal segments onto proteins using Remodel
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Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use 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 <database-path> -overwrite -out:file:scorefile model3.sc

 

The blueprint file has the following form:

<all the preceding residues listed>

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
0 x I NATRO
0 x I NATRO
<all the residues in model4.pdb treated as an insertion with EOF after last residue of insertion>

 

When it runs it runs until it quits with the following errors:

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
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
 

 

Post Situation: 
Mon, 2016-01-04 11:26
achambe