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Is there a side-program enabling us to see the clashes and interactions between ligand and protein?

Category: 
PyRosetta

I'm currently working on a program where i may need to see clashes and interactions between ligand and the protein after PyRosetta-lead conformation. Is there such program? 

Thanks!

Post Situation: 

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

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:

Post Situation: 

problem plotting results from docking_analyser with provided Rscript

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

Post Situation: 

rna_denovo secstruct_general function

Category: 
Nucleic Acids

Hello all, I had a question about how to properly use the -secstruct_general flag to input non-canonical and canonical basepairing interactions. I'm trying to test this on a simple structure from the 3IRW RNA that has a non-canonical g a basepair but I keep reseiving errors.  I am running the following command with the following files.

 

rna_denovo.static.linuxgccrelease -nstruct 1 -fasta ../test.fasta -secstruct_file ../test.secstruct -secstruct_general ../test.secgen -minimize_rna true -out:file:silent testing.out 

Post Situation: 

computing Pnear for Rosetta ligand docking

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.

Post Situation: 

Issues with angle Constraints during Docking

Category: 
Constraints

Hello,

I am setting up Docking simulations of 2 Monomers of a protein that forms monolayers at interfaces (HFBI, pdb entry 2fz6 ), so I need to constrain the possible Docking configurations to stay within the x-y plane and only beeing allowed to slightly change its orientation, due to a exposed hydrophobic patch.
I tried to use a combination of 2 angular and one Dihedral constraints. The constraint file looks like:

AngConstraint.cst:
"

Post Situation: 

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