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Design

Warnings during relax

Category: 
Design

I am getting  a lot of warnings like this:

core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 53 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 92 BRANCH 1
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
 

This is using the following relax command:

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rosetta backrub

Category: 
Design

Hello

I want to use Rosetta backrub for peptide design. by I faced an error that I think it caused to incompatible .py and .sh files and Rosetta 3.9 2018 version. I searched a lot on Rosetta website to find out any example of .py and .sh file that they need for running Rosetta Backrub. my error was ERROR: unable to open MM atom type  set file:/home/nanobio/amin/rosetta_database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt ERRoR: Exit from: src/core/chemical/MMAtomTypeSet.cc line 64".

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Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

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Docking tree issues

Category: 
Design

Hi all,

I am trying to design the interface of a peptide docked on a protein. For that, I have written a design XML considering only peptide residues to be designed. I use a docking tree mover that should define 1 jump in the sequence, but when I run the script I always get the same error:

File: src/core/pose/util.cc:1341
[ ERROR ] UtilityExitException
ERROR: Cannot compute center of mass of zero residues!

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Undocumented changes in BackrubDD

Category: 
Design

Greetings Rosetta developers,

I am trying to use BackrunDD via rosetta_scripts (Rosetta ver 3.9). But I could not help but notice the difference between the available attributes for BackrubDD  when I run ' rosetta_scripts -info BackrubDD' and those documented in the following link:

https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubDDMover.

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problem in downloading result from backrub server

Category: 
Design

Hello 

I used backrub server for flexible modeling and the results of my run sent to my email address. but unfortunately I can not download my results and I got an error. I tried to download my results in several days but I got an error again. what is the problem and how can I solve it? thanks

 

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Pyrosetta protocol to move protein-peptide docked complex closer to active site.

Category: 
Design
Enzyme Design

Hi,

I have a protein-peptide(15 a.a) system with alreaddy a good guess for the binding mode of the peptide. Now I want to move slightly the peptide to a more reactive conformation and design mutants in this reactive conformation.

The “enzdes” application with a constraint file would do exactly what I need but I think it was created for “protein-small ligand” systems and I cannot use it with a multiple residues ligand like my peptide.

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Efficient implementation of MPI with protein design programs

Category: 
Design

I'm running Rosetta single state design (though I imagine my question applies to MSD as well), which works great on a single core or my local machine.  I'm using rosetta_scripts.mpi.linuxgccrelease as my package.  It is compiled by my HPC administrator to function with the cluster.

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