I'm using pepspec to design a peptide. I've been able to run the application with some options (listed below) but my peptides always seem to fly off into space, with the exception of the region near the anchor residue. I've tried a few different combinations by looking at the application documentation, but I can't seem to get anything that looks "reasonable". My options are:
What is the difference between n_build_loop and n_cgrelax_loop? The documentation says these control the number of iterations of "global" and "local" backbone sampling but I'm not sure what these mean. Most of the designed peptide looks like it has the "default" fully-extended conformation.
Any thoughts on what I'm doing wrong? Or is this some indication that it may be difficult to design a peptide for this particular receptor?