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Docking

Dock two domains using topology broker

Category: 
Docking

Hi,

I have two domains that are asymmetric and I want to dock them using topology broker (asymmetric fold and dock like operation). Below is the full description of my problem:

1. I have pdbs for two domains that I want to dock. Domain1 has 3 chains and domain2 and 1 chain

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problems with generating the params file

Category: 
Docking

I was preparing the ligand params file for docking. When I used the following command to generate params files, I always get the "Too many arguments!" error. 

​~/rosetta*/main/source/scripts/python/public/molfile_to_params.py \ -n XX -p XXX --conformers-in-one-file XXX.sdf 

How to fix this problem? Thank you in advance.

 

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Surface Docking Crash (continued)

Category: 
Docking

Hello,

This is a continuation of an earlier thread, but I am still having trouble getting the surface_docking application to accept my inputs of a protein and ice surface. After correcting issues with hydrogen naming and now using the -ignore_waters false flag so that rosetta does not delete the ice surface, I am still getting the following error (this was all the error output):

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Filter based on ligand_is_touching

Category: 
Docking

I'm trying to predict where a small molecule ligand will dock to a dimer protein and am trying to do a completely blind search. To do so, I use the start from mover to place the ligand at the center of my protein and then the initial perturb option in the Transform mover to randomly move it outside the protein. Since the protein is not circular, depending on which direction the ligand goes, it can end up pretty far from the protein. If this is wrong, or there is a better way to do it, feel free to let me know.

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extract pdbs segmentation fault

Category: 
Docking

Hey,

So I ran a docking simulation in which I docked a small molecule to a dimer metal containing protein. I generated 1000 structures output into a  silent file. I wanted the top 10 scoring structures just to see if the run worked and used "grep '^SCORE' IPDock/IPDock.out > IPDock/IPDockScores" to extract scores, the sort command to order them and created a file with the top ten structures.

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Surface Docking Application Crash

Category: 
Docking

Hello,

(New user to Rosetta, so I apologize if this is the wrong place to post this or a silly question)

I am trying to use the Surface Docking application (https://www.rosettacommons.org/docs/latest/application_documentation/docking/surface-docking) to dock a protein to a crystal surface using only a fasta sequence file.

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