You are here

Chemically Modified Residues

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

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.

Post Situation: 

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

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.

Post Situation: 

Error reading in/out glycosylated silent file - "Can't create a polymer bond after residue due to incompatible type"

Category: 
Chemically Modified Residues

Hi all,

I'm having trouble extracting (or reading in) a previously rosetta glycoslylated structure from a silent file after relaxing it. Attempting to either extract or read back in the relaxed structure from a silent file results in the following error:

 

Can't create a polymer bond after residue 506 due to incompatible type: ->4)-alpha-D-Glcp:non-reducing_end

 

The protocol I used is as followes:

Post Situation: 

parameter file of GLU protonated (GLU_P1.params)

Category: 
Chemically Modified Residues

Hello,

I have a protonated GLU in the active site of an enzyme. I would like to use GLU_P1.params in my simulation by -extra_res_fa (the OE2 is protonated). I need to change the name of this protonated GLU in the PDB, but I am not sure what it should be. Because the NAME and IO_STRING are different and are not three letter code. Please see below and let me know what the name of this protonated GLU in the PDB file should be.

GLU_P1.params:

Post Situation: 

Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Sir and Madam,

I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.

Post Situation: 

Pages

Subscribe to RSS - Chemically Modified Residues