Rosetta Remodel – Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

[Anonymous]

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

ERROR:: Exit from: src/core/conformation/Conformation.hh line: 499

This is when i use X for residues.

In this case my blueprint file is structured like this:

1153 M .

1154 E .

0 X L

0 X L

My command is remodel.static.linuxgccrelease -s 5xwp.pdb -remodel:blueprint 5xwp.blp -ex1 -ex2 -num_trajectory 10.

When i attempt to set specific residues instead of X and use -remodel:use_blueprint_sequence with the above mentioned command i get a segmentation error (core dump).

in that case my blueprint file looks like this:

1153 M .

1154 E .

0 E L

0 K L

and my command is remodel.static.linuxgccrelease -s 5xwp.pdb -remodel:blueprint 5xwp.blp -ex1 -ex2 -num_trajectory 10 -remodel:use_blueprint_sequence.

relevant output here:

LLHHHHHHHHHHHHLEEEEEEELLLLLEEEEEEEELEEEELLLLLLLLEEEELLLHHHHHHHHHHHHLLLLLLLLLL

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat

core.scoring.elec.util: Read 40 countpair representative atoms

core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.

core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.

core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/harald/Desktop/Projectfiles/Rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin

core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/harald/Desktop/Projectfiles/Rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.13 seconds to load from binary

protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): length change found. last blueprint line index: 1160, last blueprint line original_index: 0

protocols.forge.remodel.RemodelWorkingSet: Adding lines to temp_for_truncation vector.

Segmentation fault (core dumped)

 

I do not understand what am i doing wrong. I generated the blueprint file per tutorial from the .pl script and i repeat: when i add no residues it runs fine and generates 5 structures. So it is something to do with my new residues that i am adding in the blueprint file. I tried to renumber them continuously like 1154 1155 1156 but then i get a different error in both 1155 1156 and 0 0 numbering :

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose.

ERROR:: Exit from: src/core/conformation/Conformation.hh line: 500

 

So something is wrong with the way i am typing in the new residues. But i do everything per tutorial from documentation: https://www.rosettacommons.org/docs/latest/application_documentation/design/rosettaremodel#algorithm_basic-remodelling-tasks_de-novo-structure_c-terminal-extension

 

Thanks for assistance.

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