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MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

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MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"
#1

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

rosetta_scripts.macosclangrelease -l list -ex1 -ex2 -use_input_sc -parser:protocol motifgrat_sc.xml -script_vars context=context.pdb motif=motif.pdb rmsd=5 NCrmsd=5 clash=50 hotspots=1:4:8:10,1:4:6,1:3,2:3:4 delta=0:0,0:0,2:0,1:2 independent=0

As you can see my motif.pdb structure has 4 fragments, and as I parsed the delta variable, the mover can try a few fragment sizes to fit the motif into the scaffold structure.

After a while trying to fit the structures, I got the following error:

 

...

protocols.motif_grafting.movers.MotifGraftMover: Generating a epigraft structure with overal RMSD score: 4.16317, motif maxRMDS of: 0, and clash score of: 23

core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 23

core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 24) is now out of date!

core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  

Segmentation fault: 11

...

I tried using different version of Rosetta (3.7, 3.8, 3.10) and the results are the same. I am also attaching the entire output log for the run.

Is there any troubleshooting for this?

Thanks,

Danilo.

AttachmentSize
motifgrat_sc.xml_.txt1.03 KB
output.log153.07 KB
Category: 
Post Situation: 
Mon, 2020-02-03 11:09
dfcoelho

I kind of have found the problem. I used the "editconf" tool from GROMACS to change residues numbering and chain ID for the motif fragments.

The output of GROMACS seems to be incompatible with MotifGraft mover. I didn't figure out yet why. The format of the output PDB seems fine for me. Other protocols from Rosetta work fine with the same pdb file. 

Anyway, problem solved.

 

Danilo.

Tue, 2020-02-04 07:44
dfcoelho