I wanted to model two tight turns in my protein keeping the backbone of the protein fixed. This was done to evaluate the change in the energy due to changes in loop sequence and also to look for low energy conformations. I wanted only some selected residues at those loop positions for which I made a resfile.
Here are the parameter for loop modeling :-
-resfile : resfile
-mute core.util.prof ## don't show timing info
-mute core.io.database ## don't show database info
LOOP 22 25 23 0 0
LOOP 115 118 116 0 0
23 A PIKAA HDSN
116 A PIKAA HDSN
Finally the results that I got were unexpected. Because, for the first loop Rosetta changed the last residue instead of the middle ones For eg. VNGH was changed to VNGR. I wanted to see the effect of replacing "N" with the residues mentioned in resfile. For the second loop , the sequence EDGT was changed to ENNA. Here last two were changed , I wanted the middle two only. Also, total_energy for all the structures was positive. It is the same protein (GFP, pdb id - 1GFL) that I am using for enzyme design.
How could I specifically look for the changes in only the middle two residue of a four residue loop, without disturbing the stem of loop ??