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Error: Could not find scorefxns and name score12 in Datamap in rosetta_bin_linux_2017.39.59729_bundle

Submitted by a-eatemadi@razi... on Sun, 2017-11-05 02:42
Category: 
Docking

Hi everyone,

I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:; 

 

 ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol  docking_stubs.xml

 

Post Situation: 
Solved
Forums: 
Rosetta 3 - Build/Install

How to make a resfile

Submitted by dflaher on Fri, 2017-11-03 10:26
Category: 
Docking

Hello,

I am new to using Rosetta. I would like to make a res file to mutate through all 20 amino acids in a Protein-protein interface and predict binding energy using RosettaDesign.  This might be a stupid question but how to you make a resfile? Do you write it in text edit? Is the file extention .res?

I have found the refile syntax page from Rosettas website but it does not say where you type any of the commands into or how to save it.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Ligand docking cannot open the protein file

Submitted by swarekwood on Tue, 2017-10-17 08:17
Category: 
Docking

Hi there!

I follow the ligand docking tutorial from here: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

When I get to point 6 and try to run docking protocol via ./rosetta_scripts.linuxgccrelease @options it says ERROR: Cannot open file "3PBL_ETQ.pdb"

How can I check the particular path to the file and correct, if needed?

Thanks in advance!

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Dock two domains using topology broker

Submitted by sn on Thu, 2017-10-05 17:07
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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

problems with generating the params file

Submitted by dyu on Thu, 2017-09-28 13:34
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.

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

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