Hello,
I have a question about KIC protocol. I am using the next generation protocol together with fragments. I think it should be fine but I just wanted ti double check couple of things.
Firstly, can I use fragments together with these flags? :
-loops:taboo_sampling
-loops:kic_rama2b
-loops:ramp_fa_rep
-loops:ramp_rama
-loops:kic_omega_sampling
-loops:allow_omega_move
I am just checking that there isnt some kind of “conflict of interest” between using these flags as well as the fragments.
Secondly, the flag -loops:fix_natsc, does it just stop Rosetta remodelling the side chains of neigbouring residues? Not the actual loop residues?
And finally, when I am generating fragments, am I suppose to submit the full protein seqeuence to the Robetta or just the residues that are found within the loops?
Thank you so much! I am really gratefull for your help
My full flas file:
-in:ignore_unrecognized_res
-overwrite
-nstruct 500
-constant_seed
-ex1
-ex2
-loops:remodel perturb_kic_with_fragments
-loops:refine refine_kic_with_fragments
-loops:fix_natsc
-rebuild_disulf true
#-in:detect_disulf true
-loops:taboo_sampling
-loops:kic_rama2b
-loops:ramp_fa_rep
-loops:ramp_rama
-loops:kic_omega_sampling
-loops:allow_omega_move
-loops:loop_file 4MWF.loops
-constraints:cst_fa_file 4MWF.fa.cst
-constraints:cst_fa_weight 20.0
-constraints:cst_file 4MWF.cst
-constraints:cst_weight 20.0
#-in:fix_disulf 4MWF.disulf.txt
#-packing:resfile 4MWF.resfile
-loops:frag_sizes 9 3 1
-loops:frag_files /d/as12/u/sl002/rosett/run/loop/run_1/9mers.txt /d/as12/u/sl002/rosett/run/loop/run_1/3mers.txt none
-in:file:fullatom
-out:file:fullatom
Thank you
L.
.
