Loop Modeling

Hi I'm trying to fill the missing loop with remodel.linuxgccrelease in rosetta

for some pdb, there's no problem in filling missing loop

but I got following error with certain PDB

core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLL  |  aa = .......
core.fragment.picking_old.vall.eval.ABEGOEval: abego = LLLLLLL
core.sequence.ABEGOManager: [ ERROR ] Unrecognized abego index: L

I am running loop model with the remodel protocol (remodel.static.linuxgccrelease).  It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault.  Anyone experience this before?

Hi all,

I have been banging my head against the wall on this for a while now, and I think it's time to get help.  Here is my problem.  I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me. 

I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."