I have used KIC with fragment protocol for loop modeling as follows
-loops:frag_files frags/test.200.9mers frags/test.200.3mers none
-loops:frag_sizes 9 3 1
I am using rosetta_2014wk35_bundle.
The loop file without and with extension designated as follows
1. LOOP 147 161 160 0 0
2. LOOP 147 161 160 0 1
My output have been low energy structures with unusual secondary structure and very long bond lengths for the loop modeled region (pdb001_without extension) with a loop file without extension. While with loop extension the secondary structure looks normal but atomic detail has C-O distance of ~66 Å for each residue in the loop model region see pdb002_with_extension.
Could someone help me to figure out what is causing this. I have used the CCD and Next generation KIC protocol ( with -loops:frag_sizes and -loops:frag_files) call removed) and I do get properly modeled loops see pdb003_KIC
PS: Example pdb files below need to be renamed with a .gz extension and then uncompressed as they have been compressed using gzip
Thank for your time