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Should I be stripping water molecules from my input structure for Rosetta Design?

Category: 
Design

So I've ran my fixbb rosetta design script and have been happily doing some analysis work, but it just occured to me that I had stripped all the water molecules from my input protein structure and I'm curious whether that biases the rosetta design in a negative way.

What I want to do with my project is to take a fixed-backbone structure of my choosing, optimize the sidechain identities using Rosetta, and then ultimately express it in a cell to see if the optimized sequence folds back into the original backbone conformation.

Post Situation: 

Can't generate a cst file to use with ddg_monomer application

Category: 
Design

Hi everyone,

I would like to create some double mutations in my protein and thought to get a prediction of the ddG change using Rosetta's ddg_monomer application. I tried running the preminimization using:

Post Situation: 

C-term amidation

Category: 
Design

Hello,

I have been trying to use the Cterm_amidation patch, but everytime I use it in FastDesign or scoring it turns it back into a regular C terminus.

I've read the posts from other users, but I still can't make it work... What am I doing wrong?

Things I've tried so far:

I added "-include_patches Cterm_amidation" flag, both with the input file having a regular C terminus and with a neutral terminus - in this case I made sure the names of the atoms matched these in the patch:

Post Situation: 

Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"

Category: 
Design

Hello,

I'm a new user wants to run a RosettaScripts with disulfize mover, but right after I start the scripts, I got the following crash report. Any comments or suggestions on how to solve the issues? Thanks a million.

Post Situation: 

Remodel and the depracated EMPTY NC

Category: 
Design

I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.

I am using Remodel in Pyrosetta 4 2020.49 release (a stable)  for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.

Post Situation: 

Segfault with Pepspec

Category: 
Design

Hello,

I am using pepspec to design a peptide inhibitor of a serine protease. I am using a structure of the enzyme, with a docked Arg, obtained from a crystal structure (so no Anchor Docking is needed). I want to design a peptide by adding residues to the N-terminal side of the anchored Arg. Previous pepspec, I repacked the structure with fixbb with:

Post Situation: 

cartesian delta delta G

Category: 
Design

Heya,

I am new to Pyrosetta and attempting to implement the Cartesian delta detla G paper, however i am struggling a bit with it. There is already a tutorial on delta deltaG in the official tutorials, and from my understanding the differences to the Cartesian version are simply an initial relax with a different score function (ref2015_cart) and then backbone relaxes around the mutation site. This is kinda what i am struggling with.

 

How can i relax only a certain site + 2-5 sites around it?

 

Post Situation: 

Help - Protein-Protein interface design

Category: 
Design

Hello everyone!!

I am trying to work on the protein-protein interface design using rosetta scripts.  I am new to running rosetta scripts. So, I kindly need help on that. 

I ran the configure file given in the first step which threw me an error of Nobsub in path. I tried installing bsub and adding paths to the bash file but still wasn't able to proceed further. 

Kindly help me out if there are any mistakes or details i may have missed in setting up the run.

Thanks in advance

Post Situation: 

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