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Docking

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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Rosetta-foldtree and docking

Category: 
Docking

Hello everyone,

I'm using Rosetta's docking_ Protocol does the docking of two proteins (one protein is double chain and the other protein is single chain), but when I run the command:

$ROSETTA/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking

It explains that "Cannot compute center of mass of zero residues! ". How to solve this problem?

My parameter settings are as follows:

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small ligand docking in Ubuntu 20.04, please help

Category: 
Docking

    Hi, sorry for disturbing you but  I have problems about samll ligand docking in Ubuntu 20.04. It occurs errors when I followed jens Meiler's toturial about small ligand docking.

command line:

$ ~/Desktop/rosetta_workshop/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @options.txt -nstruct 5 -database ~/Desktop/rosetta_workshop/rosetta/main/database/

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