I preform using loop modelling base of fragment database to remodel the loops of a protein,
But when it generates several models (e.g., 10000), it changes the other part of the protein (e.g., helix conformer) too.
But I expect , only remodels the loops site not other sites.
Only thing I can think of is that something is strange with your loop file or input flags. Can you post both?
Now my problem is solved , as I used this commands,
-loops:input_pdb inputs/Inactive_min_ph.pdb \
-loops:loop_file inputs/Inactive.loop_file \
-loops:frag_sizes 9 3 1 \
-loops:frag_files inputs/aat000_09_05.200_v1_3.gz inputs/aat000_09_05.200_v1_3.gz none \
-loops:remodel quick_ccd \
-loops:remodel perturb_kic \
-loops:refine refine_kic \
-loops:fix_natsc true \
-loops:neighbor_dist 0.0 \
-out:prefix Inactive_H \
-nstruct 1000 \