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Non-Canonical Peptides

Error with xml script

Submitted by almeida85 on Tue, 2023-03-28 01:53
Category: 
Non-Canonical Peptides

Hello,

I am using an xml script to design macrocycle peptides similar to https://www.pnas.org/doi/abs/10.1073/pnas.2012800118.

The script runs well in my HPC machine until it crashes unexpectedly. Attached is the output with the backtrace of the error. I am using Rosetta version rosetta.source.release-314 r314 2022.11+release.512e589 512e58946eaed9de20d65cdeea465e7690dc9e9a.

I am using the same script with a different peptide sequence and it runs well, until now.

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Rosetta 3 - General

N-Terminal Galactose

Submitted by SebastianBB on Mon, 2022-11-21 08:33
Category: 
Chemically Modified Residues
Non-Canonical Peptides

Hi,

I want to modell the HbA1c (Hb with Galactose bound to the N-Terminal Val) N-Terminal residues.

I can't find a matching paramterset for the Galactose in the database. The to6-*-*-Galp.param is very close except that instead of the O6 atom, the C6 is bound to the N of the Val.

What is the best way to add the right parameters as a new residue type? Copy the to6-*-*-Galp.param files and modify just the atoms bound to the N or start from scratch?

How would the new *.param file look like?

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Setting pivots points for GenKIC

Submitted by almeida85 on Tue, 2022-10-25 02:32
Category: 
Non-Canonical Peptides

Hi all,

I want to use GenKIC to generate macrocycles of a peptide bound to a receptor with the anchor design approach. Previously, I used simple_cycpep_predict, from the command line, to generate the candidates, but not bound to the receptor.

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Rosetta 3 - Applications

Macrocycle from a C-terminal amidated peptide

Submitted by almeida85 on Thu, 2022-08-18 07:53
Category: 
Non-Canonical Peptides

Hello,

I want to generate a macrocycle of a 10 residues peptide, that has an amidated C-terminal residue.

For this, I am playing with simple_cycpep_predict with the -cyclic_peptide:cyclization_type sidechain_isopeptide flag to get crosslinked sidechains between positions 5 and 10, i.e, LYS5 ... ASP10 (ASP10 is amidated). I have a lineal peptide pdb of the same sequence that I would use as native). My command line and flags are:

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Rosetta 3 - Applications

Problems with ICOOR when generating polymer params file

Submitted by liuwenxi on Tue, 2022-08-09 08:33
Category: 
Non-Canonical Peptides

Hello,

We're trying to incorporate a nonanonical amino acid (3, 5-Difluorotyrosine) in my enzyme design protocol. We've been using the molfile_to_params_polymer.py script provided in the demos folder; however, the params file isn't generating correctly (the file is attached below as DFT.params). When running enzyme design protocol, we get the following error:

             "Only the third ICOOR atom in a topology file should list itself as its own dihedral atom"

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Rosetta 3 - General

Unknown Element "SE" when generating NCAA params file containing selenium

Submitted by liuwenxi on Thu, 2022-08-04 16:24
Category: 
Non-Canonical Peptides

Hello,

I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.

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shape complementarity

Submitted by holdenj on Fri, 2022-07-15 13:24
Category: 
Non-Canonical Peptides

I am using the shape complementarity filter to evaluate noncanonical amino acids. For several noncanonicals that contain Chlorine and Fluorine atoms the sc value is -1. I suspect this is due to the code for sc not being compatible with atom types that are not C,N,O,S,and P. Does anyone have a solution or suggestion on how to get sc updated to work with all NCAA's?

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Rosetta 3 - Applications

Molfile to params creating invalid params output

Submitted by edan on Sun, 2021-08-29 01:54
Category: 
Non-Canonical Peptides

Hi, 

I am trying to generate a ncAA. My current workflow is using a program called iQmol which has a connection to a QChem server, to produce an appropriate mol file. I then use mol_file_to_params.py to get the params files. It creates a params file with all the atoms quite close together. Running mol_file_to_params gives me this output with the attached files:

 

edanhabel@Edans-MacBook-Pro-2 molfile2params % python molfile_to_params.py iqmol_pymol_aromatic.mol2 -n f5p --clobber --amino-acid PHE

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PyRosetta - General

NCAA attached at two points

Submitted by tsztain on Wed, 2021-06-16 15:20
Category: 
Non-Canonical Peptides

Hello,

I am trying to parameterize an NCAA which is a result of cyclization of the backbone, rather than just a PTM of an R group. I am using the molfile_to_params_polymer.py script (BTW is there a python 3 version of this script?) 

The connection points are at the R group of one residue, though there is a break in the chain (C=O -> C-OH) then a connection point to the nitrogen backbone atom of the subsequent residue.

When I use fixbb to modify to this residue I am getting the error:

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