I have some questions about rosetta design. I have been trying to use rosettaDesign "fixbb" to design a cyclic-peptide that binds to an enzyme. Here are the questions I have:
1) No matter what amino acid sequence I start with and how many iterations I run, the 100 output structures from each iteration always end up with the SAME UNIQUE sequence. How to interpret this?
2) In the output sequence, there are many GLY residues, which doesn't produce any meaning interaction with the enzyme. Are there any flags missing in my run?
3) The N- and C-termini are supposed to be covalently-bonded since it's a CYCLIC peptide. However, the output from rosettaDesign always produce FREE termini. Is there any way to force the NT and CT to be connected?
Here are the flags I used:
-design -fixbb -read_all_chains -fa_input -repack -ex1aro -ex2aro_only -resfile myresfile -pdbout -ndrun 100
Thank you in advance,