You are here

Home

Docking

Error while reading in silent file

Submitted by rweisse on Mon, 2015-04-20 00:31
Category: 
Docking

Hi all, I am facing an error, when reading in the silent output file after a docking simulation. Here I used 6 cores to create 2000 decoys each (sum 12000). See the flag file attached. I used a slightely modified version of the ligand docking application, which is provided in the ROSETTA examples.

Now, i tried to combine all six output files to compare the results. Actually, I tried it with the following command

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Relax command for docking purposes and cluster_vs_rmsd command

Submitted by Rkfoury on Wed, 2015-04-01 08:48
Category: 
Docking

Hello All,

I currently have two questions.

The first related to using the relax.linuxgccrelease,

I am relaxing a cleaned native structure to produce a 1000 decoys, in which I will cluster and use the top 5 to perform docking with Rosetta.

My question is when I relax my native structure, what options and flags should I include and not include. Should I be relaxing with contraints on the main chain and side chains, or should I relax with no constraints. Should I include -ex1 and -ex2aro flags for my purpose? Should I perform relax:fast or relax:thorough?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Unrecognized residue Glc

Submitted by cgautier on Tue, 2015-03-31 02:20
Category: 
Docking

Hi everyone,

I would like to use surface_docking on a pdb containing carbohydrates.
I put as residue name "Glc" in my pdb and I added the flag:

extra_res_fa=/media/storage/a/software/rosetta_src_2015.02.57538_bundle/main/database/chemical/residue_type_sets/fa_standard/residue_types/carbohydrates/to4-beta-D-Glcp.params

However I get the following error:

ERROR: No match found for unrecognized residue at position 1
Looking for lower-terminal residue with 3-letter code: Glc
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1216

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Docking with Constraints in PyRosetta

Submitted by protos_heis on Sat, 2015-03-28 11:16
Category: 
Docking

Recently I started attempting to use PyRosetta to perform protein-protein docking. I was following the PyRosetta docking tutorial at www.pyrosetta.org/tutorials and managed to get a script together that can generate a bunch of coarse models and then the best n of them are submitted to high resolution refined docking.

Post Situation: 
Unsolved
Forums: 
PyRosetta - Applications

Executing the clean_pdb.py script

Submitted by Rkfoury on Fri, 2015-02-20 10:16
Category: 
Docking

Hello All,

I am currently running RosettaCommons on linux and am attempting to run the clean_pdb.py script on my native protein.
As of now, I have changed it to an executable file as recommended, but I am unsure what the command is to run this script on a certain pdb.

As of now my command is $ python clean_pdb.py script path/to/pdb, but this doesnt appear to be correct. Can anyone direct me on what the script requires for a command and exactly what to type in so it runs it on my vinculin.pdb protein.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?

Submitted by cossio on Thu, 2015-02-05 07:10
Category: 
Docking

docking_prepack_protocol generates several output pdb structures:

away__*_0001.pdb
away_packed__*_0001.pdb
initial__*_0001.pdb
prepack__*_0001.pdb
*_0001.pdb

where * stands for the name of the crystal structure that was given as input to docking_prepack_protocol.

What are the differences between these .pdb files that docking_prepack_protocol outputs?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Reproduce Robetta's ddg values of interface alanine scan using Rosetta?

Submitted by cossio on Mon, 2015-01-19 07:14
Category: 
Docking
Scoring

Is there a protocol on Rosetta to obtain Robetta's (http://robetta.bakerlab.org/) ddg's calculations of interface alanine scan functionality?
I don't care if they use an older version of Rosetta. I just want to obtain ddg's values that are as close as possible to those returned by Robetta. What protocol do they use?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches

Submitted by zaldini on Fri, 2015-01-02 05:53
Category: 
Docking

Hello,
I would like to know how to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches?
In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other new linear peptide structures at this same binding site, in order to run the docking calculations using the rosetta3 protocols.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Docking