# Docking

## Global ligand docking with Rosetta script and PyRosetta

Category:
Docking

Hi all,

Is it possible to perform global ligand docking with Rosetta script not PyRosetta?

I found the tutorial for global ligand docking in PyRosetta. ( https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb )

But, I could not find any explicit example for global ligand docking with only Rosetta script.

Thank you,

Post Situation:

## Rosettasurface in Pyrosetta 4

Category:
Docking

Greetings,

I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.

Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4?

Thanks very much!

Hao

Post Situation:

## Problems with waters in CoupledMoves application

Category:
Structure prediction
Docking
Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

Post Situation:

## PIPER-FlexPepDock protocol file apply_ftresult.py missing

Category:
Docking

Hello,

I've been trying to run the PIPER-FlexPepDock pipeline in both ways, following the steps in the documentation page (https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock), and using the scripts in the "tools/peptide docking" folder. But both cases need the script "apply_ftresults.py" which doesn't exist in the source. Where can I get this script or any equivalent?

Post Situation:

## Cterm_amidation

Category:
Docking

Hi there,

I am trying to run Flexpepdock for several peptides which have Cterm_amide group. I checked the ATOM TYPES for NH2 which are also correct but while reading pdb it always gives warning:

Post Situation:

## Python2 script in Rosetta3.13

Category:
Docking
Good morning,

I am trying to use Rosetta (v3.13) for  drug screening analysis and I
found a specific script in the Rosetta3.13 package (also in other
versions) which has some python2 code that hampers its use in the
current python3.

The script is:
rosetta_bin_linux_2021.16.61629_bundle/main/source/scripts/python/public/batch_molfile_to_params.py

Python2 code:

1) Lines 110, 114, 117: print without brackets

2) Lines 40, 116: "is not" instead of "!="

Post Situation: