I have a structure. I do homology modeling of another target. The template has a peptide of length 9. The new target that I am modeling has a peptide of length 10. When I perform the modeling, the target misses that 1 residue of the peptide. Is there a way to add that residue to the end of peptide?
I tried various things:
1. Adjusting the alignement (this always messes up something) before using rosetta_cm.
2. Rosetta Remodel. I gave the blue print file with one residue indicated as insert, but doesn't seem to go through due to:
protocols.forge.remodel.RemodelDesignMover: (0) Creating NeighborhoodByDistanceCalculator using und_pos: [ ]
protocols.forge.remodel.RemodelDesignMover: (0) Warning: union_of_intervals_containing_undefined_positions() returned empty set. NeighborhoodByDistanceCalculator could return undefined results.
Is there any other way model the target correctly?