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Segfault with docking protocol

Submitted by almeida85 on Mon, 2021-02-08 06:39
Category: 
Docking

Hello,

I am trying to run the docking protocol for a high resolution local refinement, but I get a Segmentation fault error. The command is

docking_protocol.linuxgccrelease -partners A_B -docking_local_refine -database $ROSETTA_DB -in:file:l list.txt -ex1 -ex2aro -use_input_sc -out:file:silent decoys_high_res_refinement.silent -out:file:silent_struct_type binary -out:path:score score_high_res_refinement.sc -out:prefix high_res_ref_ -out:nstruct 100

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Rosetta 3 - General

Problem with protein and ligand preparation before ligand docking.

Submitted by zg148119@ohio.edu on Fri, 2021-02-05 06:47
Category: 
Docking

Hello,

I have a problem with cleaning my protein before ligand docking. I use the command clean_pdb.py 1i09 A to download and clean GSK-3, but the final structure has some missing residues, even more than the initial structure in the protein data bank. There is no gap in the AA sequence when open the structure as a text file, but using PyMol, there are dotted lines instead of solid lines in some areas of the structure. I have uploaded the initial and the cleaned PDB files for your consideration.

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Rosetta 3 - General

There is a problem executing “rosetta_scripts.static.linuxgccrelease ”

Submitted by zjya on Tue, 2021-02-02 23:44
Category: 
Docking
import subprocess
def minimize(working_directory):
    subprocess.run([rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease,
        f"@{flags_relax.txt}",
        f"-parser:protocol",
        f"{dock_relax.xml}"',
        "-database","rosetta/main/database/],
        cwd=str(working_directory))

The above is the program I used.When I use rosetta_scripts.static.linuxgccrelease command to minimize pdb, but the following warning appears and the program cannot be stopped:

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Rosetta 3 - General

problem plotting results from docking_analyser with provided Rscript

Submitted by madammolecular on Mon, 2021-02-01 14:44
Category: 
Docking

hello,

I was performing protein protein advanced docking from tutorials and I did docking_analyser.xml protocol and got docking_analysis.csv with all scorings and now I have trouble making plots in R with provided script sc_vs_rmsd.R . I have tried Rscript sc_vs_rmsd.R docking_analysis.csv total_score but it outputs error "Must request at least one colour from a hue palette." I would appreciate very much if some one could help me. thank you

 

jovana

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Rosetta 3 - General

computing Pnear for Rosetta ligand docking

Submitted by rohi on Mon, 2021-02-01 08:27
Category: 
Docking

Hello,

I am calculating the Pnear for the Rosetta ligand docking outputs to evaluate the funnel-likeness of energy vs RMSD by treating the lowest energy model as the native structure. Is it right to use binding energy and ligand RMSD (no superposition) as E and RMSD in Pnear formula? I see in the papers it is used for de novo designs and they use the total energy and general RMSD.

I really appreciate your help.

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Rosetta 3 - General

[Solved] Resetting a pose with RigidBodyTransMover

Submitted by bjharris on Wed, 2021-01-13 14:01
Category: 
Docking

I'm trying to seperate a protein-protein complex, apply residue labels based on core/surface/boundary layer definitions, and then reset the protein-protein complex for design. My first thought was to use the RigidBodyTransMover, however, I cannot perform the reverse rigid body translation to recombine the protein-protein complex; the ouput file has the proteins out of contact. I'm unfamiliar with the coordinates, but am noticing that the end coordinate differs after back transformation:

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Rosetta 3 - Applications

protein-ligand docking rescoring with interfaceAnalyzer

Submitted by syntekabio2019 on Sat, 2020-12-19 03:59
Category: 
Docking

 Hi 

 My name is Jong hui Hong

 I'd like to rescore docking result structure made by Rosetta-script application with InterfaceAnalyzer

 But InterfaceAnalyzer application binary couldn't be found in binary folder ( rosetta-source/main/source/bin) .

 Is there any other folder for that application ?

 It seems that InterfaceAnalyzer source is there in Rosetta source

 Can there be something wrong with my rosetta installation?

 Any kind of suggestion or answer would be appreciated 

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