Rosie Docking Server-Energy function
Submitted by jsv on Fri, 2017-07-21 08:26
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Docking
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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SNUGDOCK
Submitted by adva on Sun, 2017-07-16 00:46
Category:
Docking
Hello,
I tried running snugdock on ROSIE. The run finished and when I downloaded the output files from the server, I got this messge in the output.json file:
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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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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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Error Interface analyser
Submitted by jrcf on Thu, 2017-06-22 12:55
Category:
Docking
Hi people,
I'm trying to use the interfaceAnalyzer, but this error is showing.
This is the script I run
obs. I don't know why the output score doesn't make.
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Adding water interactions when docking a ligand with Rosetta 3.7.
Submitted by brspurri on Thu, 2017-06-01 09:37
Category:
Docking
I am using RosettaScripts to dock a ligand, and I would like to include several - known - key water interactions.
I found a demo somewhere (RosettaCon?) that showed this is possible, but I it looked like the xml was designed for a version well before Rosetta 3.7. From reading the Scripts docs, it looks like including the term minimize_water=true to the <MOVEMAP_BUILDER /> element should handle the water interactions.
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Error in a new docking
Submitted by jrcf on Wed, 2017-05-17 19:26
Category:
Docking
Hi guys, I need a little help.
I run a docking, and I had a great result.
So, I repeat, but change the initial position of one of the proteis.
When I run, this error is showed.
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Regarding the efficiency of the new low resolution ligand-docking movement “Transform”.
Submitted by Martin Floor on Mon, 2017-05-15 09:19
Ligand Docking with RosettaScripts gives a ParsedProtocol exception
Submitted by brspurri on Sun, 2017-05-14 17:51
Category:
Docking
I am trying to run a ligand docking simulation, and am running into a few technical limitations. I am trying to follow the tutorial form the Meiler lab (only with a different starting pdb and ligand).
I am running the command:
rosetta_scripts.linuxgccrelease -database $ROSETTA_DATABASE -in:file:s /inputs/4XXX_model.pdb /inputs/MyLigand.pdb -in:file:extra_res_fa /inputs/MyLigand.params -nstruct 3 -parser:protocol /scripts/xml/dock.xml -mistakes:restore_pre_talaris_2013_behavior true
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