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Docking

IL-2 gets better binding with beta / gamma

Category: 
Docking

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.   

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Residue outside res_map range

Category: 
Docking

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.

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Error: Start tag expected, '<' not found

Category: 
Docking

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.

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protein location change during Docking protocol

Category: 
Docking

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:

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problem in using "zinc_site_redesign" tool

Category: 
Docking

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:

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RosettaDock 4.0 ambiguous ERROR

Category: 
Docking

Hi all,

I'm running a protein-protein docking (both partners are ~240 res. monomers) and I get the following error:

---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

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