# Docking

## Protein Ensemble RosettaLigand Docking

Category:
Docking

Dear Rosetta Users,

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

Samuele

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## RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()

Category:
Docking

Dear Rosetta Users,

I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:

[FILE]: src/core/conformation/util.cc

[LINE]: 654

[START_MESSAGE]

[ ERROR ] UtilityExitException

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## Chain name being read as residue

Category:
Docking

Hi,

I am attempting a ligand docking run in a P450 docking both the heme cofactor and ligand simultaneously. I was able to have a successful run with just the heme group but when I attempt to add in the ligand I get an error. Currently, I've been getting the error "unrecognized mm_atom_type_name W" where W is the chain name for my ligand. I've attached my docking file, initial structure pdb file, and my options file so they can be looked at to help me resolve this issue. Thanks in advance!

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## Argument Error while running Ligand_interface.py

Category:
Docking

Hello,

I am facing trouble running the script ligand interface.py. I have prepared the pdb file and params file as instructed. I have also added the params file to the default directory and updated residue_types.txt file. The following error gets invoked. Please do help rectify the error.

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## How to write down a connection between ligand's atom and metal ion from enzyme?

Category:
Docking
Small Molecules

Dear Sir or Madam,

Post Situation:

## 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

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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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## 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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## 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: