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Protein Docking Error

Submitted by ac.research on Thu, 2017-08-17 02:57
Category: 
Docking

Dear All,

 

I am learning how to do protein-ligand docking and I am following the Rosetta built-in tutorial: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

 

I did not change anything whatsoever. I used the same tutorial files (as is) and attempted to run the calculation as such:

{PATH_TO_ROSETTA}/main/source/bin/rosetta_scripts.linuxgccrelease @options

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Rosetta 3 - General

Produces a set of rotamers from a given residue

Submitted by a-eatemadi@razi... on Tue, 2017-08-15 08:05
Category: 
Docking

Dear Rosettaers

I would like to dock Individual residues against the target surface on my protein. In this way, I have to produce a set of individual hydrophobic rotamers which can bind to a hydrophobic pocket on my protein. 

I used this RosettaScript to generate inverse rotamers:

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Rosetta 3 - General

Issues with residues and structure changing with FlexPepDock; is this normal?

Submitted by rnelson on Tue, 2017-08-08 10:06
Category: 
Docking

This is probably a silly question so I apologize if so, but recently lab has been investigating some novel interaction sites between a protein and peptide based off of recent crosslinking and IP data. I created some pdb files of the protein and the peptide aligned at the various novel and established crosslinking sites and submitted them to FlexPepDock to see if the models were reasonable.

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Rosetta 3 - General

SNUGDOCK

Submitted by adva on Sun, 2017-07-16 00:49
Category: 
Docking

Hello,

I am trying to run SnugDock locally, and I follow the well explained demo. I noticed that makefab.pl script is missing. It should be in the demo / rosettascripts directory but its not there. Also, there is a link in the README.md file but its blocked by a usename and password....

Can anyone help?

 

Thanks,

Adva

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Rosetta 3 - General

Some problems with the "advanced protein-protein docking" tutorial

Submitted by Sunyp_IM on Tue, 2017-06-27 09:33
Category: 
Docking

I am studying the Rosetta "advanced protein-protein docking" tutorial (https://www.rosettacommons.org/demos/latest/tutorials/advanced_protein-protein_docking/advanced_protein-protein_docking_tutorial), but I find some confusing problems with it. 

Problem 1

The input file pdb file for the docking  command: 

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Rosetta 3 - General

Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking

Submitted by Sunyp_IM on Sun, 2017-06-25 02:40
Category: 
Docking

Dear all,

I am learning the advanced "protein-protein docking" part of the Rosetta about the docking of HA and antibody. When I input the following command in this tutorial: 

$ROSETTA_TOOLS/protein_tools/scripts/pdb_renumber.py --norestart input_files/3GBM_AB.pdb input_files/3gbm_HA.pdb

I get the following error message:

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