I am trying to model several loops and the N-terminus of my protein at the same time using the pose-based loop modeling with CCD closure.
This works fine for the loops, but not for the N-terminus, which causes rosetta to crash. From the wiki page:
"Terminal loops can also be specified in a similar fashion, but obviously no chainbreak will be introduced."
In my loops.txt file I added a line
1 24 0 1
my command line is
rosetta.exe aa 1FOO A -s 1FOO -pose -loops -fold_with_dunbrack -pose_loops_file loops.txt -ex1 -ex2 -fa_input -fa_output
If I just have the N-terminus, rosetta crashes. If I only specify the other (non-terminal) loops, it works.
Is this supposed to work?