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## Segfault with docking protocol

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 $ROSETTA_DB -in:file:l list.txt -ex1 -ex2aro -use_input_sc -out:file:silent decoys_high_res_refinement.silent -out:file:silent_struct_type binary -out:path:score score_high_res_refinement.sc -out:prefix high_res_ref_ -out:nstruct 100 Post Situation: ## slurm not availble Category: Compilation Good afternoon, I am attemtpting to compile according to item 1.5.1 at https://csrosetta.chemistry.ucsc.edu/node/1354...$ module load   python/2.7 slurm openmpi/gcc/64

however slurm is not available. The cluster uses PBSPro. Can anyone suggest a work-around?

Thanks - Dave Morgan Ph.D., Colbert Lab, NDSU

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## Problem with protein and ligand preparation before ligand docking.

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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## 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:

Category:
Nucleic Acids

hi all,

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## 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:

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## 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

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## 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

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## 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.