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Design

Fixing part of a ligand in dock-design

Category: 
Docking
Design

Hi,

 

I am using a dock-design protocol to design a binding pocket to bind a ligand. I know where parts of the ligand should bind (orinetations and the position in protein) but the other parts can be flexible. Right now after the dock and design protocol, most of my outcomes change the whole position of ligand and don't keep that part fixed. Is there a way to tell the program to keep parts of the ligand fixed? or a way to generate conformers for only parts of the ligand? 

 

Thanks.

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Protein/Protein Ddg demo: How to write predicted mutant structures?

Category: 
Structure prediction
Design

I am following the protein/protein Ddg demo:

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

I am wondering if there is a way to modify the script mutation_script.xml so that I can write the predicted structures of the mutants to PDB files?

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What is "repack", "prepack"?

Category: 
Structure prediction
Docking
Design

All over the place in Rosetta Documentation, I find the terms "repack", "prepack". But I have not found their definitions. I suspect that "repack" and "prepack" refer to conformational samplings where only amino acid side chains are moved, while the backbone remains fixed, but I can't be sure. Is it in this sense that these terms are used here?

What are the definitions of "repack" and "prepack" (in the common usage of these terms in the ROSETTA community)?

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pose.replace_residue() & incorrect scoring

Category: 
Design
Scoring

Hi developers,

I wasn't sure where to submit bug reports so I'm posting here instead.

I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.

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fixbb algorithm reference?

Category: 
Design

Hi,

I'm interested in understanding how the fixbb application works. It mentions in the documentation page:

https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d4/d68/fixbb.html

a stochastic simulated annealing approach is used. However, I do not see a description of this approach in the references on that page.

I did find a reference to a Metropolis Monte Carol procedure here:

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ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL, when running minimize_with_cst.linuxgccrelease

Category: 
Design

This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):

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loop modeling

Category: 
Design

Hi,

I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn't read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:

flag file:

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