Hi,
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:
-pepspec::soft_wts soft_rep.wts
-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0
-pepspec::n_peptides 1000
-pepspec::n_cgrelax_loop 10
-pepspec::n_build_loop 1000
-pepspec::diversify_pep_seqs
-pepspec::diversify_lvl 100
-ex1
-ex2
-extrachi_cutoff 0
-pepspec::save_low_pdbs
-pepspec::pdb_list /Volumes/MacintoshHD2/james/input/input.docked.pdblist
-pepspec::pep_chain B
-pepspec::pep_anchor 295
-pepspec::n_prepend 10
-pepspec::n_append 10
-o receptor_spec
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?