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Chemically Modified Residues

Model GFP chromophore(cro) using NCAA or NC backbone method?

Submitted by lei on Thu, 2024-04-04 06:23
Category: 
Chemically Modified Residues

Dear users,

Because GFP chromophore (CRO) comes from cyclization of three amino acids: S, Y, and G, I am not sure how to model it.

(1) In "Using NCAAs in Protein-Peptide Interface Design", Ornithine can be seen as a modified form of Lys: only one amino acid.

However, CRO includes three amino acids, so there are total three R groups. When preparing rotamer library, CHI angles from three R groups seems confusing.

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Rosetta 3 - Applications

analyze_flex_ddG.py

Submitted by valebut on Tue, 2023-11-28 04:30
Category: 
Chemically Modified Residues

Hello,

I am new to Rosetta. I am trying to perform the Flex ddG tutorial in order to predict changes in binding free energies upon mutation (interface ΔΔG).

I downloaded the folder from the GitHub webpage, and I  succeesfully ran the run_example_1.py script which has generated three folders with one rosetta.out files (along with other files).

Then, I ran the python3 analyze_flex_ddG.py output/ command, and I get this error:

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Rosetta 3 - Applications

nomenclature question in molfile_to_params_polymer.py in ncaa design

Submitted by lei on Tue, 2023-11-21 09:47
Category: 
Chemically Modified Residues

Dear users,

In NCAA tutorial, in order to use molfile_to_params_polymer.py script, we have to update the mol file by adding some additional data at the end of mol file.

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Rosetta 3 - Applications

RECCESS-Rosetta Segmentation Fault with nonnatural residues

Submitted by skorro on Tue, 2023-07-25 17:13
Category: 
Chemically Modified Residues

Hello,

 

I am trying to run the recess-turner function with the following command:

recces_turner.macosclangrelease -score:weights stepwise/rna/turner -seq1 gu  -seq2 [2MA]c -recces:n_cycle 9000000 -recces:temps 0.8 1 1.4 1.8 3 7 30 -st_weights 9.024828183205116 18.24157438187578 22.310063998885838 25.608533286161883 25.949659063278826 25.027484033009934 -recces:out_prefix ST -save_score_terms 

 

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Rosetta 3 - Applications

Post-traslational modifications

Submitted by diegoms on Wed, 2023-06-21 01:22
Category: 
Chemically Modified Residues

Hello, everyone

I was trying to study the effect of post-translational modifications on the structure of proteins. For that purpose, I followed two different approaches:

  1. I modified the residue with a variant using pyrosetta.rosetta.core.pose.add_variant_type_to_residue. Then, I replaced the original residue with the modified one using pose.replace_residue().

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PyRosetta - 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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Rosetta 3 - General

Modelling at defined pH - for pmutscan - pH:mode not working

Submitted by cagfa1 on Tue, 2022-03-15 04:05
Category: 
Scoring
Loop Modeling
Chemically Modified Residues

Hi all, 

I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.

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Rosetta 3 - Applications

RAbD with N-term，Proline-like ncaa returns segmentation fault during CCDEndsGraftMover

Submitted by CordycepsLin on Sun, 2022-02-06 19:09
Category: 
Design
Chemically Modified Residues
Fragment Generation

Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope. 

I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.

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Rosetta 3 - Applications

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