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Non-Canonical Peptides

Macrocycle from a C-terminal amidated peptide

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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Problems with ICOOR when generating polymer params file

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

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

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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Molfile to params creating invalid params output

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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NCAA attached at two points

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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adding NCAA to the N-terminal of RCSB pdb

Category: 
Non-Canonical Peptides

Hello,

I usually use my NCAAs by mutation in the sequences. 

Now, I am looking for a way or application in Rosetta to add, not mutation, NCAAs to the N- terminal and C- terminal of the sequences. 

The RCSB pdb starts with leu at N- terminal in attached picture that we need to add pyroglutamate before that 

 I wonder if anyone could let me know how I can add pyroglutamate using params file and rotlib file to the sequence. 

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Patch to impose tetrahedral geometry on backbone O atom

Category: 
Non-Canonical Peptides

Hello,

I want to model the tetrahedral transition state of an enzyme where serine OG attacks the peptide backbone C atom. In this case the bond order of the backbone C=O bond changes to C-O(H) and the C-O(H) is not in plane anymore.

So far I wrote this patch file and added a hydrogen to the O atom in the input model which is named H01. The patch file is used since I get an error when I don't include it.

 

BEGIN_CASE

BEGIN_SELECTOR
NAME3 LEU
END_SELECTOR

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params file for beta-amino acids

Category: 
Non-Canonical Peptides

Hi all,

I've been trying to insert a beta-amino acid into peptide, let's say, beta-homo-leucine. It seems that a params file for beta-hLeu is needed. Unforutnately, there is no params file for beta-hLeu in database in Rosetta, and molfile_to_params.py only works for alpha-amino acid. I've also visited https://rosie.rosettacommons.org/documentation/beta_peptide_design, but did't find helpful solution. So my question is:

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