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Docking

SnugDock Partners parameter

Category: 
Docking

Hello everyone,

I recently read in the manual that "partners" parameter must be set in the order of how they are set in the PDB. However, I was unaware of this previously and set my partners as LH_A, while my pdb files are ordered as HLA. The docking is working and has been running for a couple days, but I am wondering if this will affect the results of the docking?

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How to add new Movers to Rosetta

Category: 
Docking

I have a folder with some files to define a mover 'AddEncounterConstraintMover' the Path of the folder is  under 'source/src/devel'. What should I do to make Roseta 'read' the files and apply the mover when its runninng? I have all .hh, .cc, .fwd.hh and Creators files.

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Problem with 'AddEncounterConstraintMover'

Category: 
Docking

Greetings, I'm trying to reproduce a local protein-protein docking using replica exchange methods published in this paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010124

After I run I receive  the followinf error message:

 

[FILE]: src/protocols/rosetta_scripts/RosettaScriptsParser.cc

[LINE]: 1192

[START_MESSAGE]

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Local docking- should I use KIC?

Category: 
Docking

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

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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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