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Chemically Modified Residues

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

Altering substrate specificity

Submitted by bp on Thu, 2016-12-22 02:45
Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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Rosetta 3 - Applications

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