Hi, I'd like to include some NCAAs in my peptide design. I can use a resfile in which I disallow the canonicals and write NC to allow for unnatural residues:
EMPTY NC
start
However, if I want to allow certain NCAAs, how can I know the 3-letter code that corresponds to each NCAA??
Thanks!!
Salva
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Post Situation:
Unfortunately, there's not necessarily a systematic way of figuring that out. (Rosetta doesn't necessarily use any standard naming scheme for the NCAAs.) Generally speaking, you should refer to the params file of the particular NCAA you want. Most NCAAs aren't enabled by default in Rosetta, so you'll have to track down the params file (and rotamer library) that corresponds to the one you want. Once you have that params file, you can examine the IO_STRING line in the params file to figure out what the 3-letter code for that NCAA/params file is.