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
.
