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Docking

Ligand Docking with ROSETTA

Submitted by sc19 on Thu, 2022-07-14 01:32
Category: 
Docking
Small Molecules

Hi,

I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:

1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.

2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.

3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).

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Rosetta 3 - Applications

SnugDock Partners parameter

Submitted by tyang39 on Fri, 2022-07-08 10:02
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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Rosetta 3 - Applications

How to add new Movers to Rosetta

Submitted by mb0261 on Thu, 2022-06-30 10:48
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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Rosetta 3 - General

Problem with 'AddEncounterConstraintMover'

Submitted by mb0261 on Tue, 2022-06-28 10:00
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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Rosetta 3 - General

Local docking- should I use KIC?

Submitted by seayoung lee on Fri, 2022-05-27 02:45
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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Rosetta 3 - Applications

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