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Chemically Modified Residues

patch file modification for ser_phosphorylated.txt

Submitted by hajar on Sun, 2020-06-21 00:49
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:

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Rosetta 3 - General

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

Submitted by matteoferla on Sun, 2020-02-16 06:27
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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Rosetta 3 - General

Problems when working with PTMs - cannot make sugar poses

Submitted by MNP1986 on Thu, 2019-01-10 07:44
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.

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PyRosetta - Applications

Chemically bound ligand connection error

Submitted by tsztain on Tue, 2019-01-01 18:40
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 

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Rosetta 3 - Applications

molfile to params polymer python errors

Submitted by tsztain on Sun, 2018-12-02 15:38
Category: 
Chemically Modified Residues

I am trying to generate parameters for a non-cannonical amino acid using the molfile_to_params_polymer.py script using python 2.7.5.python molfile_to_params_polymer.py --clobber --polymer --no-pdb --name OCT -k OCT.kin OCT.mol

Edit: this is where I found the python script that is giving the errors.  /path/rosetta_demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py

I get the error:

Traceback (most recent call last):

  File "test_molfile_to_params_polymer.py", line 1995, in <module>

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Rosetta 3 - Applications

Using residue patches in AbinitioRelax

Submitted by kent on Fri, 2018-11-02 11:19
Category: 
Structure prediction
Chemically Modified Residues

I am hoping to 'fold' short phosphorylated peptide sequences, and started by generating fragments with SS predictions on the unphosphorylated peptides. For example, I ran this sequence through a local installation of PSIPRED and picked 200 3- and 9-mers:

>1
MKGDAHRYLAEFATG

I checked that the TYR_p:phosphorylated patch was active in the full-atom patches.txt, then created a centroid patch and added it to the patches.txt by analogy to existing patches:

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Rosetta 3 - Applications

Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Submitted by dasdevashishdas on Thu, 2018-08-16 21:15
Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

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Rosetta 3 - General

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