Domain insertion with Non-CAA

Hi all,

I am trying to insert a long fragment (GFPStrand) into another protein (4e1s) using Remodel. I’ve delete the residues that were originally in 4e1s but left a few at the end as an anchor for the domain insertion. Remodel throws an error about insertion indices being 0 if I don’t leave them to anchor it. Remodel accepts the domain insertion and starts on the loop closure. It also appears to close the loop, but then throws this error with trace: 

protocols.forge.remodel.RemodelMover: 

protocols.moves.MonteCarlo: MC: 2  16.1898  13.0953  16.1898  13.0953  0  0  0  accepted score beat last

protocols.moves.TrialCounter:         ccd_move trials=    225;  accepts= 1.0000;  energy_drop/trial=  -0.02888

protocols.moves.TrialCounter:             frag trials=   1660;  accepts= 0.5687;  energy_drop/trial=   0.00549

protocols.forge.remodel.RemodelMover: ** boost_closure_stage

core.chemical.ResidueType: Residue dstor

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.chemical.ResidueType: Residue dstor

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom TYR:protein_cutpoint_upper OVU1

loops: adding loop LOOP start: 226  stop: 249  cut: 249  size: 24  skip rate: 0  extended?: True

loops: 

core.chemical.ResidueType: Residue dstor

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL1

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom ALA:protein_cutpoint_lower OVL2

core.chemical.ResidueType: Residue dstor

core.conformation.util: copy_residue_coordinates_and_rebuild_missing_atoms: missing atom TYR:protein_cutpoint_upper OVU1

protocols.forge.remodel.RemodelMover: at least one loop is beyond tolerance

protocols.forge.remodel.RemodelMover: * 1 / 1   closed / attempts 

core.chemical.ResidueType: Residue dstor

core.chemical.ResidueType: atom name :  HE1 not available in residue CRO

core.chemical.ResidueType: ‘ CA2’ 0x7fca92e844c0

core.chemical.ResidueType: ‘ CB2’ 0x7fca92e84810

core.chemical.ResidueType: ‘ CG2’ 0x7fca92e84b80

core.chemical.ResidueType: ‘ CD1’ 0x7fca92e84f50

core.chemical.ResidueType: ‘ CE1’ 0x7fca92e851f0

core.chemical.ResidueType: ‘ CZ ‘ 0x7fca92e85710

core.chemical.ResidueType: ‘ CE2’ 0x7fca92e85970

core.chemical.ResidueType: ‘ CD2’ 0x7fca92e85c20

core.chemical.ResidueType: ‘ OH ‘ 0x7fca92e85f00

core.chemical.ResidueType: ‘ C2 ‘ 0x7fca92e86570

core.chemical.ResidueType: ‘ O2 ‘ 0x7fca92e86800

core.chemical.ResidueType: ‘ N3 ‘ 0x7fca92e86ae0

core.chemical.ResidueType: ‘ CA3’ 0x7fca92e86dc0

core.chemical.ResidueType: ‘ C  ‘ 0x7fca92e870a0

core.chemical.ResidueType: ‘ O  ‘ 0x7fca92e87380

core.chemical.ResidueType: ‘ C1 ‘ 0x7fca92e87660

core.chemical.ResidueType: ‘ CA1’ 0x7fca92e87940

core.chemical.ResidueType: ‘ CB1’ 0x7fca92e85500

core.chemical.ResidueType: ‘ CG1’ 0x7fca92e862d0

core.chemical.ResidueType: ‘ OG1’ 0x7fca92e87c60

core.chemical.ResidueType: ‘ N  ‘ 0x7fca92e87f40

core.chemical.ResidueType: ‘ N2 ‘ 0x7fca92e88220

core.chemical.ResidueType: 

core.kinematics.FoldTree: slide_cutpoint: current= 246 target= 249 FOLD_TREE  EDGE 1 225 -1  JEDGE 225 250 1 N C  END  EDGE 250 251 -1  EDGE 225 246 -1  EDGE 250 247 -1 slide_cutpoint: final tree= FOLD_TREE  EDGE 1 225 -1  JEDGE 225 250 1 N C  END  EDGE 250 251 -1  EDGE 225 249 -1 

ERROR: unknown atom_name: CRO   HE1

ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 3540

I’m relatively certain it’s trying to go from centroid back to full atom, but I’m not sure. My fragment pdb is full atom, including hydrogens on the CRO residue. rmoretti had attached a centroid version of CRO somewhere else in the forums that I’ve supplied as a flag and am reattaching below. The full atom version is in residue_types/extra/CRO.params. 

Any ideas what I’m missing? If I don’t need those anchoring residues, that would be great too. Is it just too large a “domain”? My full set of flags are below. Thanks!

Meghan

-s 4e1sShort.pdb

-remodel:blueprint 4e1sShort.blueprint

-extra_res_fa /extra/CRO.params

-extra_res_cen CRO.cen.params

-run:chain A

-remodel:domainFusion:insert_segment_from_pdb GFPStrandRenumbH.pdb

-remodel:RemodelLoopMover:bypass_closure #If I don’t have this flag, it makes 50 CCD attempts and seg faults

-remodel:RemodelLoopMover:boost_closure_cycles 0 #Changing this number doesn’t affect my error.

-ex1

-ex2

-use_input_sc

-out:file:scorefile remodel.fasc

-in:file:spanfile 4e1s_A_spansShort.txt #This gets read in easily, so the membrane part isn’t the problem

-membrane:no_interpolate_Mpair

-membrane:Menv_penalties

-membrane:Mhbond_depth True

-membrane:thickness 12.5

-score:weights membrane_highres_Menv_smooth

-mute core.scoring.MembraneTopology

#-out:levels protocols.loops:trace

-out:levels all:trace