Hello everyone, I would like to ask, how to add the following lines when creating a parameter in the rosetta for a non-standard amino acid containing a methyl group on the backbone? M ROOT 13 M POLY_N_BB 13 M POLY_CA_BB 14 M POLY_C_BB 15 M POLY_O_BB 16 M POLY_IGNORE 2 3 4 5 6 8 9 10 11 12 M POLY_UPPER 7 M POLY_LOWER 1 M POLY_CHG 1 M POLY_PROPERTIES PROTEIN POLAR CHARGED M END
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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?
So...a bunch of other posts says to just rerun it if Rosetta fails with "cannot normalize xyzVector of length() zero". But what if you DO get this error consistently across different runs with different seeds? Like, every time? Where should I start looking to even solve this problem? I'm running EnzDes in Rosetta 3.8 (working on updating to 3.10), and it fails here. I am using a NCAA and a water molecule in the active site.
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:
However, if I want to allow certain NCAAs, how can I know the 3-letter code that corresponds to each NCAA??
If I run this command:
residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true
on the attached pdb, I get this error:
Hi all, I'm trying to run relax on a pdb which has ACE and NME terminal caps. Is there a way I can preserve those in the output? I'm not an expert Rosetta user, but here are some more specifics of what I've tried: