I rebuilded two missing loops in a crystal structure and tried to use Rosetta to refine these loops. I want to refine the loops but keep the rest of the native structure (both backbone and side chain) "freeze". However,each time the loops were repacked, the neighbor residues connect to the loops will also move. I tried to fix the native structure with -loops:fix_natsc, and also try to set the neighbor distant to 0, but all failed.
The command was:
./loopmodel.linuxgccrelease -database ../rosetta_database/ -loops:input_pdb 2wuy.pdb -loops:loop_file 2wuy.loop -loops:remodel perturb_kic -loops:refine refine_kic -ex1 -ex2 -nstruct 10 -loops.max_kic_build_attempts 100 -in:file:fullatom -loops:fix_natsc true -loops:neighbor_dist 0.0
and the loop file was:
LOOP 31 49 40 0 1
LOOP 173 187 180 0 1
If I want to fix the original structure and optimize the rebuilded loops, what should I do?
Thank you very much!