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Chemically Modified Residues

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

Submitted by amorin on Mon, 2021-09-27 12:16
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:

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Rosetta 3 - Applications

parameter file of GLU protonated (GLU_P1.params)

Submitted by rohi on Sat, 2021-06-05 20:44
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:

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Rosetta 3 - General

Protocol for adding/mutating non-canonical AA

Submitted by joeri on Thu, 2021-03-25 08:14
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. 

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PyRosetta - General

Protocol for adding/mutating non-canonical AA

Submitted by joeri on Thu, 2021-03-25 08:14
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. 

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PyRosetta - General

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

Submitted by Corvin on Wed, 2020-12-16 04:58
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.

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Rosetta 3 - Applications

Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Submitted by Corvin on Wed, 2020-12-02 04:00
Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Rosetta people,

I am trying to dock ligand, which possesses by sulfonamide NH group to the target protein with a help of coupled_moves application by the following command:

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Rosetta 3 - Applications

Prevention of the negatively charged Nitrogen protonation by coupled_moves

Submitted by Corvin on Wed, 2020-11-18 02:56
Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear sir and madam,

I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:

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Rosetta 3 - Applications

BuildPeptide - Using Phosphorylated and Sulfated Tyrosine

Submitted by jlawrie on Thu, 2020-09-03 14:29
Category: 
Chemically Modified Residues

Hello,

I am trying to build to both phosphorylated and sulfated tyrosine containing peptide squences to use for docking. Unfortunately, I am unable to use the BuildPeptide command to construct these peptides as aI always recieve a Segmentation Fault error. I would appreciate any help. I have been trying to convert the starting fasta sequences: GY[TYR:phosphorylated]EEIA and GY[TYR:sulfated]EEIA without any luck. I have been able to construct the unmodified peptide, GYEEIA, successfully.

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Rosetta 3 - Applications

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