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Non-Canonical Peptides

simple_cycpep_predict issue modifying terminal residue

Category: 
Non-Canonical Peptides

Hi, I'm trying to use simple_cycpep_predict to model the conformation of a disulfide linked cyclic peptide. The peptide has an amidated C terminus. I've been trying to get the patch Cterm_amidation working however it appears to ignore the patch.

A sample input sequence is:

CYS ALA ALA ALA ALA CYS ALA ALA ALA:Cterm_amidation

And here's my test input script:

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adding greek_alphabets in non-canonical AA parameter generation

Category: 
Non-Canonical Peptides

Hello

I am running molfile_to_params_polymer.py to get the .params file for my non-canonical aa. But I got the error below. I think it might be due to the long chain of my non-canonical amino acid. I tried to increase the greek letters list in line 1655 of the script, but it did not work. Maybe it needs to modiy several lines of code.

Also, I got large numbers (as you see the error below).Can someone help to modify the code for my non-canonical  amino acid to resolve the error?

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cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues

Category: 
Non-Canonical Peptides

Good evening,

I am experiencing an odd behaviour with the cartesian_ddg application (Rosetta version 3.11) when trying to specify multiple simultaneous mutations to non-canonical residues in the mut_file.

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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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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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