Reply To: RosettaDesign (each run produces the same sequence with many GLY residues )

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May 13, 2009 at 6:27 pm #4088
Anonymous

    > 1) It means the packer really likes that sequence. How large is the sequence space you’re searching? How many rotamers? If it’s small you may be searching it exhaustively.
    >
    > 2) It probably means you’re getting a lot of sidechain clashes. Look up the soft_rep_design flag and see if it helps (it softens VDW repulsion).
    >
    >

    Thank smlewis very much for the comments. Here are the answers to your questions:

    1) My cyclic peptide is 8-residue long. I would expect some sequence like F-E-K-A-R-V-R-R that satisfy surrounding environment (TRP, TYR, ASP, SER, GLN,…), but what I got is always P-G-G-G-D-G-G-G. How to find out “how many rotamers”?

    2) The first sequence to start with is A-A-A-A-A-A-A-A, so I would think there shouldn’t be many sidechain clashes. I’m going to try “soft_rep_design”.