I am trying to use the RosettaRemodel Application to insert three residues into a structure. I want the backbone structure to have a loop structure. However, for some reason I am getting a warning in the output file. Originally there was a residue within the structure where these residues are but I manually removed them. I removed this residue because because it wasn't an amino acid but a molecule. My overall goal is to delete the molecule from the pdb and insert three amino acids in its place. So the total pipeline goes something like this. I removed the molecule in the structure, I renumbered the structure (so it starts from 1 and is continuously numbered), and then I ran RosettaRemodel on the pdb structure. I kept the chain id since it is only a single chain.
The blueprint file I used looks like:
57 T .
58 L .
59 V .
60 T .
61 T L PIKAA L
62 L L PIKAA L
0 x L PIKAA T
0 x L PIKAA Y
0 x L PIKAA G
63 V L PIKAA V
64 Q E PIKAA Q
65 C .
66 F .
My flags look like:
-database -database path_to_database
The warning I get is:
protocols::checkpoint: (1) Deleting checkpoints of LoopMover
protocols.forge.remodel.RemodelMover: (1) design_refine: final chainbreak = 0.337903 at 66
protocols.forge.remodel.RemodelMover: (1) WARNING: DESIGN REFINE FAILED TO CLOSE STRUCTURE!!
protocols.forge.remodel.RemodelMover: (1) Remodel poses remaining from original run: 0
protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Finished job successfully! Sending output request to master.
protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 30
I am not sure why I am getting this warning and what exactly it means. Does this mean that the design failed and that the inserted loop region could not be closed? I tried designing residues on either side of the inserted region to help but for some reason the warning persists. Am I doing something incorrectly? Any help would be appreciated.