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revert_design_to_native app comparison to FavorNativeResidue mover

Category: 
Design

Hello,

I am currently designing ligand-binding protiens, but designs are returned with more mutations than I would like. In order to reduce this number, I currently use the revert_design_to_native app, but I recently read about about the FavorNativeResidue mover. However, I am unsure of the differences in function between the two. I made two small sets of designs with the FavorNativeResidue bonus set to 0.5 and 1.5, and I ran revert_design_to_native on those designs with the same thresholds, respectivley. 

Post Situation: 

Loop design with length variation

Category: 
Design
Loop Modeling

hi all,

I am working on protein design for antibody-antigen complex to improve the binding affinity. so far, I have the crystal structure of the antigen (chain A) and the antibody Fab (chain H and L). now I want to re-design part region of one CDR loop (around 5 residues) involved in direct interaction to antigen. besides the design for the loop retaining original length (5 AA), I also try to make the loop shorter or longer with the randomizing the residues of loop.

any suggestion that where I can start from?

many thanks,

Post Situation: 

New parametrization problems

Category: 
Design

Hello all!

I started working with my non-canonical residue REL and found out that it doesn't bond to other residues.

Shall I write some other atoms in the end of mol file?

I am afraid only visualization can help here so I attach the mol file.

Also I attach the created with this mol file params file and one molecule with REL residue.

Thank you in advance,

Dmitrii

Post Situation: 

Parametrisation problems

Category: 
Design

Hello everyone!

I have a residue in my protein, that is non-canonical and that I named REL.

After all the steps from https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README with the only difference in using molfile_to_params.py instead of molfile_to_params_polymer.py, because the second doesn't work in my rosetta suite.

Post Situation: 

-RBSegmentRelax:cst_wt not present in ca_to_allatom.linuxgccrelease application?

Category: 
Design

 Hey,

I am using Rosetta to build my protein from Ca-trace to all-atom, and then to refine this structure against cryo-em density.

However, when I use these two flags:- RBSegmentRelax::cst_wt 1.0  and -RBSegmentRelax::cst_width 4.0, I am getting the error:

Option matching -RBSegmentRelax:cst_wt not found in command line top-level context

When I remove these two flags, everytging works perfectly.

So, my question is: do these two flags are still used by ca_to_allatom application?

Post Situation: 

Submitting job to local cluster

Category: 
Design

Hi All,

I have installed rosetta on our institute cluster with mpi support (extras=mpi). I want to run rosetta script on the cluster (favor_native_residue.xml). Can anyone kindly let me know how to do it. Attached is a script i used to submit gromacs job in the same cluster (originally it was gromacs_job.sh but I changed it to gromacs_job.txt to attach here) and my favor_native_residue.xml (changed to favor_native_residue.txt for attachment). 

 

Thanks a lot.

 

Post Situation: 

Give preference to native residue during fixed backbone designing

Category: 
Design

Hi,

I want to do fixed back-bone design. Rosetta output gives me a lot of mutation. I want to limit the numbers. I donot want mutations that marginally stabilizes the protein. Is there any way to tell to software to prefer the native aminoacid. 

 

Thanks a lot

Post Situation: 

Errors in scorefiles after running Design

Category: 
Design

Hi,

I've successfully run Rosetta Design using the April 14th, 2014 weekly release (this is the latest weekly release that I can faithfully use, given the age of our cluster) on a large number of scaffolds. I've attached the options file (femoco2.txt) as a reference.

Post Situation: 

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