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RifGen error on rosetta, "assertion failed", please help!

Category: 
Design

Hi, everyone, sorry for disturbing! I ran into a error when I ran rifgen program to generate RIF residues for Patchdock.

commands line: $RIFDOCK/build/apps/rosetta/rifgen @input/rifgen.flag > rifgen.log 2>&1

results:

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Flex_ddG突变设计

Category: 
Design

Hi all:
I am using flex_ddG to enhance interface binding by mutating an amino acid on a small peptide, running rosetta gives me results, but when I run the analysis python script to try to analyze the results I get an error as follows.
Problem Description。

File" /home..../analyze_flex_ddG.py",line 215 ,in <module>

  analyze_output_folder(folder_to_analyze)

File " /home/..../analyze_flex_ddG.py",line 194,in analyze_output_folder

 ddg_score_dfs.append(apply_zemu_gam(ddg_scores))

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Dimeric interface redesign

Category: 
Design

Hi all,

I would like to redesign the dimeric interface using the heterodimer structure of protein A and protein B. I searched several protocols and saw how to increase affinity or stability by fixing one of them and changing the other. However, I want to increase the binding affinity between the two proteins by changing both sides at the dimeric interface. Anyone know how to do that? Has this method been tried before? If there are papers or protocols that I can refer to, please let me know.

Any help will be very appreciated.

Best,

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Pepspec error

Category: 
Design

Hello,

I am using pepspec in design mode, working with a peptide bound to a protein pocket. When I run the command (pepspec.linuxgccrelease -database $ROSETTA_DB @spec.args) I get the following error:

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

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about “protein mimic designer”

Category: 
Design

Hi everyone, has anyone used the program protein mimic designer? I imitated the article "De novo design of potent and selective mimics of IL-2 and IL-15" to design IL-2. In the first step, I got a lot of pdb files and stored them in the folder 01_results_scaffoldsMimicsIL2/debug. I I don't know if this result is correct, because there is an error at the end of the program running: segmentation fault (core dump).
If anyone has done it, what is the result of your first step?

The results of my first step

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Question about remodelling

Category: 
Design

I am new to Rosetta. And we hope to redesign a protein and let it easier to dock with another two protiens.  Hope to verify if my approach is correct here.

Step 1) I applied the Rosetta protocol - remodel and create the blueprint file by "~/rosetta/main/tools/remodel/getBluePrintFromCoords.pl"

Step 2) Edit the blueprint file and apply the commands ALLAAxc to all residues. 

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AddMembrane Mover Segmentation Fault

Category: 
Design

Hello,

I am using Recon MSD. I have run it functionally for a few months but now it is not working. When I try to run my bash script I get an error at the same point every time. It is during the "AddMembrane" step of my Rosetta Scripts protocol. I have tried countless tweaks to my inputs and my scripts but the same segmentation fault happens at the same time every run. 

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score against rmsd plot of designs

Category: 
Design

Hello, friends,

I was designing the "interface" (possible contacts) of a fusion protein using FastDesign. Since I was running the appliction on a laptop, so far only 200 designed models have been genrated.

I then went on to analyze the result anyway and tried to plot Score VS caRMSD (as shown in the attached file). Here are my questions:

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