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core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 24) is now out of date!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