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Modeling protonated histidine

Category: 
Design

Hi,

I'd like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1.  I see there's a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params).  What's the best way to specify in my pdbfile that I want that particular histidine to be protonated?

 I tried renaming the residue to "HIP" in my pdbfile and changing the first few lines of that param file to be:

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Running CstFileToTheozyme for Mono-Atomic Metal

Category: 
Design

Hi everyone,

I'm running into issues making a proper .cst file for a mono-atomic metal ion. I've tried to follow Wang, et. al. 2010 Protein Science paper, but am cannot get it right. I've attached my cst and flags files.

I've also attached the error file that comes up when I attempt to run CstFileToTheozyme.

The ZN.params file has been very slightly modified to have NAME ZN2 and IO_STRING ZN2 Z.

Thanks!

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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. 

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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,

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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

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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.

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-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?

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