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:
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))
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,
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.
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
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.
Hi Steven, Rocco, et al.,
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:
Hello,
I am trying to get RECON multistate Design going and have run into an issue. I have made my RECON xml script and a bash script:
I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.
My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?
code 1:
