-database /path/to/database

#IO
-loops::input_pdb 1FNA_preextend.pdb
-out::prefix 1FNA_extended

#packing to taste
-ex1
-ex2
-ndruns 10

#necessary for some stupid reason
-in::file::fullatom
-out::file::fullatom

#tell loops what to do
-loops::loop_file loopsfile_AAAA
-loops::build_initial
-loops::remodel perturb_kic
-loops::intermedrelax no
-loops::refine refine_kic
-loops::relax no
-loops::frag_sizes 9 3
-loops::frag_files  1FNA_AAAAinsert_9mer.gz  1FNA_AAAAinsert_3mer.gz