I want to model some loops and the n-terminus of a protein.
The n-terminus is 45 residues long and I know the positions of the residues 14-20.
So I have created a homology model of my protein with these residues in correct position and now want to use Rosetta to improve the loops and the n-terminus before and after these 6 residues that I know.
But when I run the simulation, exactly this 6 residues are missing and I can't explain why. I have now tried many things, especially I tried all posibilities with the loop file but nothing changed. And yes, the residues are really there in the pdb file.
What have I done wrong / how could I solve this problem?
I also have an additional question:
What is the meaning of the third number in the loop file? In the manual I find that it is the "Cut point residue number". Could someone explain me what is meant by this? I couldn't find any further information.
Thank you very much for your answers!!!
My input file and my loop file are like this:
-loops:input_pdb mc4.pdb \
-loops:loop_file mc4.loop_file \
-loops:frag_sizes 9 3 1 \
-loops:frag_files mc4_09 mc4_03 none \
-loops:remodel quick_ccd \
-loops:refine refine_kic \
-loops:relax fastrelax \
-nstruct 10 \
-out:prefix mc4 \
LOOP 1 13 13 0 0
LOOP 20 44 0 0 0
LOOP 104 118 0 0 0
LOOP 187 190 0 0 0
LOOP 262 274 0 0 0