Non-Canonical Peptides

Design with non-canonical amino acids (NCAA)

Category:
Non-Canonical Peptides

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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MakeRotLib

Category:
Non-Canonical Peptides

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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MakeRotLib

Category:
Non-Canonical Peptides

I have a about MakeRotLib quenstion:

when I run $ROSETTA3/bin/MakeRotLib.static.linuxgccrelease -database$ROSETTA3_DB -options_file C40.in，Error is as follows：

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MakeRotLib

Category:
Non-Canonical Peptides

I have a about MakeRotLib quenstion:

when I run $ROSETTA3/bin/MakeRotLib.static.linuxgccrelease -database$ROSETTA3_DB -options_file C40.in，Error is as follows：

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Consistent XYZvector length() zero failure in EnzDes

Category:
Enzyme Design
Non-Canonical Peptides

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.

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Question on Designing with NCAAs

Category:
Non-Canonical Peptides

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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Amino acid post-translational modifications

Category:
Non-Canonical Peptides

Hey all :)

Does the Rosetta force field incorporate parameters for PTMs such as hydroxyproline and C-terminal amidation? If so, where can I see this in the database? If not, how can I parameterize this?

Thanks!

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"caught exception" for PDB with membrane "DUM" residues

Category:
Scoring
Membrane
Non-Canonical Peptides

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:

caught exception

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