# Docking

## multi ligand docking using rosetta script

Category:
Docking

Hi all.

I'm trying to dock  my ligand with HEM to CYP using rosetta script with XML protocol

overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and  ligand as separate entity

But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.

For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score

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## Ligand being read as part of protein structure

Category:
Docking

Hi,

I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error:

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

chain_id W does not exist

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## 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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Category:
Docking
Small Molecules

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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

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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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