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Docking

small ligand docking in Ubuntu 20.04, please help

Category: 
Docking

    Hi, sorry for disturbing you but  I have problems about samll ligand docking in Ubuntu 20.04. It occurs errors when I followed jens Meiler's toturial about small ligand docking.

command line:

$ ~/Desktop/rosetta_workshop/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @options.txt -nstruct 5 -database ~/Desktop/rosetta_workshop/rosetta/main/database/

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Docking mover

Category: 
Docking

Hello, I have been reviewing the docking movers to perform both types, global and local. I have been testing them for a while now and with the active options to perform the global docking first, very little movement and exploration of the protein is observed in the output, the disturbances are practically local instead of global, this occurs both for DockingProtocol Mover and for Docking Mover. Would I have to first use DockingInitialPerturbation Mover or else use global docking flags and then use DockingProtocol or Docking for local?

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ligand dock into HEM containg pdb

Category: 
Docking

 Hi all

 I would like to dock  unknown chemical into PDB which have HEM as a cofactor

 But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>
                        <ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
                </RESIDUE_SELECTORS>
.

.

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charge grid in rosetta ligand docking using rosetta script

Category: 
Docking

 

 Ho all

 Recently I'm trying to do protein-ligand docking with rosetta scripting interface

 what I want to do is to incorporate charge grid in rosetta script xml file as shown below

                 <SCORINGGRIDS ligand_chain="X" width="25" name="charge">
                        <ChargeGrid grid_name="charge" weight="1.0"/>
                </SCORINGGRIDS>
.

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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,

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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

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