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Chemically Modified Residues

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.

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Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

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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Prevention of the negatively charged Nitrogen protonation by coupled_moves

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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BuildPeptide - Using Phosphorylated and Sulfated Tyrosine

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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patch file modification for ser_phosphorylated.txt

Category: 
Chemically Modified Residues

Hello,

I have a modified residue named SPF in my pdb which is composed of Serine + Phosphopanthenine arm +acyl with SMILES  below.

I noticed phosphorylated SER exist in Rosetta database. Therefore,  I decided to model this modified residue by modifying ser_phosphorylated.txt patch file. My new patch and pdb file file has been attached.

After relaxing the pdb file with the option -extra_patch_fa ser_phosphorylated_acyl.txt in the following way:

Post Situation: 

I generated a table of images & info of the premade NCAA params in the database

Category: 
Chemically Modified Residues

I don't have a problem*, I just wanted to link to a possibly useful resource. Namely, I was playing around with primeval genetic codes and I wanted to to know what the 3-letter code was for one amino acid. As a result I wrote a small script to make a table of images, filenames and three letter codes.

https://github.com/matteoferla/Display-of-preset-Rosetta-NCAAs

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Problems when working with PTMs - cannot make sugar poses

Category: 
Chemically Modified Residues

Hello everyone,

I have a protein which has a few PTMs in the form of sugars, and I have therefore started experimenting with sugars in PyRosetta. I have found a very nice guide:

https://graylab.jhu.edu/pyrosetta/downloads/documentation/RosettaCarbohydrate_Tutorial-Demo.pdf

which I have used as a starting point together with the documentation e.g.

Post Situation: 

Chemically bound ligand connection error

Category: 
Chemically Modified Residues

I am following the protocol for Relax Around A Chemically Bound Ligand

/path/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -s AcpP-TesA-C8.pdb -in:file:fullatom -extra_res_fa ./LG.params -cst_fa_file chemical_bond.cst -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -overwrite 

and I get the error 

Post Situation: 

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