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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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RemodelMover() and the blueprint file

Category: 
Design

Hello people,

 

I my attempt to get a working RosettaDesign protocol, I have come across the RemodelMover() class.

 

From the Rosetta C++ documentation, the RemodelMover should take a blueprint file in order to specify which residues to remodel. but the RemodelMover() class in PyRosetta has no method to input a blueprint file nor a resfile.

 

on its own the RemodelMover works without any errors, but would remodel the entire structure.

 

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Multistate design output

Category: 
Design

Hi all,

Sorry to trouble again.

I understand that the multistate design protocol outputs structures where the chains A and B will become AA, AB and BB.

However, I get the output of chains A and B even in the output files AA and BB.

May I find out how I could produce the output files AA and BB homodimers?

Is this something to do with my corr file?

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Error while converting mol2 to params using molfile_to_params.py

Category: 
Structure prediction
Docking
Design

I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get. 

 

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Multistate design on Rosetta - no generations produced

Category: 
Design

Hi,

I am currently running a multistate design protocol (mpi_msd.linuxgccrelease) for bispecific antibody design. After I have run the protocol with my options, the program runs and is "stuck" at this point for a long time:

core.pack.pack_rotamers: built 39485 rotamers at 58 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DoubleLazyInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 22325380 bytes

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