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