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Using NCAA

Submitted by ate on Sat, 2021-05-01 02:22
Category: 
Design

I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation , I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31”  it shows there is no parameters for C-N-C-CA

I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsions (i.e., importing 0      1 180.00 for related parameter in mm_torsion_params.txt)

 

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Rosetta 3 - General

Speeding up FastDesign

Submitted by ebetica0 on Wed, 2021-04-28 13:08
Category: 
Design
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="r15" weights="ref2015.wts"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <True name="full_pose"/>
  </RESIDUE_SELECTORS>
  <TASKOPERATIONS>
    <ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/>
  </TASKOPERATIONS>
  <MOVERS>
    <FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
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Rosetta 3 - General

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

Submitted by chrisHKL on Wed, 2021-03-24 14:22
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.

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Rosetta 3 - Applications

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

Submitted by ctqwong on Sat, 2021-03-13 03:53
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:

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Rosetta 3 - Applications

C-term amidation

Submitted by tttt on Tue, 2021-03-02 07:46
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:

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Rosetta 3 - General

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

Submitted by zhoubin on Sun, 2021-02-28 08:51
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.

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Rosetta 3 - General

Remodel and the depracated EMPTY NC

Submitted by matteoferla on Fri, 2021-02-26 07:12
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.

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Rosetta 3 - General

Segfault with Pepspec

Submitted by almeida85 on Thu, 2021-02-11 02:56
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:

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Rosetta 3 - Applications

cartesian delta delta G

Submitted by patcD on Wed, 2021-02-10 01:46
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?

 

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PyRosetta - General

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