# Design

## Help with file in article Kemp elimination catalysts by computational enzyme design

Category:
Design

Hello, I would like to ask for some help, regarding the article Kemp elimination catalysts by computational enzyme design, you would still have the transition state calculated by gauss, I need the output because I am trying to replicate the article, and I need the coordinates of the hydrogen being removed from the carbon in the transition state. Does anyone have these outputs?

Att. Thank you

Post Situation:

## pmut and scoring

Category:
Design

Hello all,

I am doing semi-rational design of my protein. So far I have one mutation that increases thermostability identified in vitro. However, Rosetta didn't predict this mutation in pmut scan. When I scored the protein variant with this mutation, the score was better than all the mutations predicted by Rosetta.

Post Situation:

## the question about ddg of disulfide bond mutants

Category:
Design

I want to evaluate the ddg between WT and  disulfide bond mutants

1. I try to use ddg_monomer and fond it does not suport it

2. Then I build disulfide bond mutants with moddler, and then  try to use ddg_monomer to evaluate  the ddg ( mutant  CYS  recovery to the amino acid of WT), and it does not work , too.

3. Just as 2.  I try to use another APP, cartesian_ddg ， and  disulfide bond mutants as the star model，and  ddgs seem is similar(just try three mutant)

Post Situation:

## Topobuilder segmentation fault

Category:
Design

I'm following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I'm in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault.

Post Situation:

## How to make .frags files

Category:
Design

Hello!

I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).

How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!

Post Situation:

## Rosetta Double changing mmCIF chain ID

Category:
Design

Hi everyone!

Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?

Best and thank for any help,

Victor

Post Situation:

## Rotate chain

Category:
Design

I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains.
This structure features a cross-like conformation, interacting at known residues.
I want to rotate each of the domains 15º along the z-axis
Post Situation:

## Using NCAA

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)

Post Situation:

## Speeding up FastDesign

Category:
Design
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="r15" weights="ref2015.wts"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<True name="full_pose"/>
</RESIDUE_SELECTORS>
<ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/>
<MOVERS>
<FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
Post Situation:

## 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: