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Predicting structure of protein after a few mutations

Category: 
Structure prediction

Hi all,

I am attempting to predict the structure of a protein after mutating a couple residues (4-5). I have the wildtype structure so I have been adding the mutations one-by-one in pymol, with each single mutation relaxed with the relax function. Is this the best way to use Rosetta to predict such structures? Also, are there any modifications to the relax function that would increase the accuracy for structure prediction?
 

Thank you!

Post Situation: 

unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file

Category: 
Membrane

Dear Users,

I am trying to use the "mp_span_from_pdb.default.linuxgccrelease" binary for generating a "span" file to be used as the input for the "predic_ddg.py" python.

However, I face the following error when I start the command.

I face no issues when trying with the demo pdb file. Yet, when I use my pdb (attached), it crashes with the following error.

Could you please help me know what the problem is and how to resolve it?

Thank you

The error:

Post Situation: 

Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol

Category: 
Membrane

Dear users,

I am trying to run the RosettaMP application to predict the effect of several mutations on the stability of a membrane protein. I am following this documentation to do that :"https://www.rosettacommons.org/docs/latest/application_documentation/membrane_proteins/RosettaMP-App-MPddG"

However, I can not locate the "compute_ddg.py" in the expected derectory (source/src/python/bindings/app/membrane/compute_ddG.py).

Post Situation: 

Help to understand docking results

Category: 
Docking

Dear colleagues, everything's ok?

I have done a docking experiments between enzyme and inhibitor.

I did global docking on cluspro web serve, following did a local and refine docking procedure.

Wight parameters, I should look to compare the docking results with my kinetics data

total score X rms; I_sc X Irms or something else?

I ask for help because some results appear so artificial.

Thanks any way

Ricardo

 

Post Situation: 

RosettaDock output

Category: 
Docking

Hi, now Iam havin gsome trouble about the RosettaDock app.

Few months ago when I proceeded the docking app, I got about 1,000 model resuts as output.

Now I get only 1 model output even though I used same input model and protocol.

Anyone can help me or having same problem with me?

Thank you!

Post Situation: 

Score.sc file showing total score 0 for all protein structures created

Category: 
Scoring

Hello, I am trying to use Rosetta to design the interface of my protein and would like to rank the predicted structures based on their scores however, after running the job, all the files show 0 for the total score. Could anyone take a look at my xml script and flags file (in the pdf file) to see if I'm missing something or how else to fix this issue? Thanks in advance!

Post Situation: 

Loop modeling

Category: 
Loop Modeling

Hello, 

I have a basic question about loop modelling. Can I use the edges as cutpoint or they should be excluded?

For instance, if my loop goes from residues 100 to 109, can residue 100 to be a cutpoint?

Thank you in advance,

Roberto

Post Situation: 

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