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Non-Canonical Peptides

Library of unnatural amino acid parameters

Category: 
Non-Canonical Peptides

Hello,

I am interested in modeling the changes to a protein after substitution of the unnatural amino acids L-ANAP and Aladan pictured below.

ANAP and Aladan

It does not appear that the params for these are packaged with Rosetta. However, is there an unofficial library/repository of Rosetta params that may contain params for these amino acids?

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Rotamer Library Generation in Rosetta3

Category: 
Non-Canonical Peptides

I have been stuck on the problem of generating rotamer libraries for a while now as I try to repeat the process for non-canonical residues (starting with the test case of ornithine [C40]).  The original documentation for this process is provided at the following address:

https://www.rosettacommons.org/demos/latest/public/make_rot_lib/README

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Enzyme Design with additional covalent backbone bonds

Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

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non-canonical residues parametrisation

Category: 
Non-Canonical Peptides

Hello!

I want to use a molecule with retinal in Rosetta. I've read the documentation on this page

https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README

But I also wanted to ask if I can somehow use the retinal parametrisation I already have for namd. There it is written in the CHARMM Parameter File.

Thank you in advance,

Dmitrii.

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​​B​3​-protein design using rosettaScript movers

Category: 
Non-Canonical Peptides


Hello everyone,
I am tryi​ng to perform a ​​B​3​protein​ design tests ​using ​rosettascript (rosetta demo model). I have 3 ​designable ​positions ​and I am interested in the functionalit​ies​ of ​the movers:​"RandomMutation" and "GreedyO​ptMutationMover​"

Using these movers, none of my design positions have been taken into account as a designable! In the log file, there are warnings
indicating that there is no design position.

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Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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