I do not how should select the score term. It seems that they give totally different results.
For the three parameters used in CAPRI, fnat, lRMS and iRMS, can they be calculated without the native model?
Hi
what are the dependencies of mol2genparams.py scripts? when I am trying to run the scripts, its saying no module name Type or BasicClasses and so on.
I already have numba, scipy and numpy installed.
Thank you
Dhiraj
Hi, I'm kind of new to Rosetta.
I am trying to dock GPCR and G protein complex using local docking, but it turns out that there is some clashes between Interloop 2 and G alpha subunit. How can I solve this problem? Should I use KIC for loop modeling and then use local docking application?
Could you please help me solve this problem?
Thank you
Hi All,
How do you generate parameters for a stapled helix peptide? The residues that are "stapled" are alanines at positions 1 and 5, inclusive. The "staple" is a 8-carbon linker. The flanking residues are all natural amino acids.
Thanks!
We would like to restrcuture the IL-2 for better binding with receptors - beta and gamma. We used tools to restructure IL2 and get a list of different variants. i.e. a list of PDB files. We hope to use computation method to find out the limited list of best structures before going to lab. So that we can focus on best group first to save time and resource.
Hello,
I have been trying to dock a ligand into my protein but I am getting two different errors. The first time I ran sbatch launch_design.sh and it would time out and give the files pocket-183006.err and .out, but the out file was empty. I tried running multiple jobs by creating a new file RosettaDesign.sh but it would fail, and I got the files pocket2-198770.err and .out. The error I received is residue outside res_map range. I have uploaded the files in text form and was wondering what is causing it to fail.
Hi everyone,
The program reported error after I typed in ~/rosetta/source/bin/rosetta_scripts.linuxgccrelease @options
[END_BACKTRACE]
[FILE]: src/protocols/rosetta_scripts/RosettaScriptsParser.cc
[LINE]: 1203
[START_MESSAGE]
Input rosetta scripts XML file "dock.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options.
Hi
I've been wondering why docking protocol moves protein which i dont want to be moved
so in my case, I have a complex PDB file with chain A, B, and C.
A is a small protein, and B and C is neighboured together, and C is the receptor
What i want to do is docking A to C, while B and C is not moved or designed.
so i made a xml script like below:
Hi everyone,
I want to dock a transition state model at the zinc site of human carbonic anhydrase II and redesign the protein. According to the paper (Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777.), I use ~/rosetta/tools/zinc_site_redesign module to do my job. Cleaning of PDB was successful, but when I tried to align the protein PDB with my transition state model, error occured:
