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How do I use the rotamers of natural amino acids instead of non-standard amino acids when designing non-standard amino acids?

because I see "The ROTAMER_AA params file line allows you to skip the MakeRotLib step if you want to let your tyrosine related NCAA use tyrosine rotamers"

for example,Non-standard amino acids pTyr is instead of Tyr, IWhat parameters should I add in pTyr.params?

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Sun, 2019-07-28 20:08

If you want the pTyr residue to just use the same rotamer library as if it was TYR, you simply have to add a line saying `ROTAMER_AA TYR` to the pTyr.params file, instead of the various NCAA rotamer lines. The one thing to be careful about is that the CHI definitions for your noncanonical residue need to match up with the definitions of the canonical amino acid you're stealing the rotamers from. If they don't, you might not get the sampling you were expecting.

As an aside, Rosetta should already be able to model a phosphotyrosine residue as a modification of tyrosine. Simply add your P/O1P/O2P/O3P atoms to the input structure in the appropriate place (with a residue designation of TYR),  and the Rosetta PDB reading code should automatically read it in as a phosphotyrosine. -- If you need to have a residue type name for your input, it would be TYR:phosphorylated.

Mon, 2019-08-26 15:00