I have docked a ligand with a perticular receptor and obtained the most stable 10 binding place. i need to visualize the binding site using pymol and i only can input pdb files to pymol. how can i make pdb containing both the receptor and ligand docked to a particulate place.i have found a way to do that using autodock tools.
thank you.
Why not try downloading Maestro (Schrodinger's visualizer) which is free?
You can download it here: https://www.schrodinger.com/maestro
You can open the results in maestro and visualize it there, without having to export them into single pdb. Of course, you can also do that in maestro if you wish.
Look under the Plugin in PyMOL. There should be a Autodock/Vina plugin. If it's not already there, you can install it via plugin manager or you can just download and install from here (https://pymolwiki.org/index.php/Autodock_plugin). Using this plugin you can prepare, run and analyze docking in PyMOL using AutoDock/vina.
For Vina output, you can simply open the output .pdbqt files in PyMOL and then open the .pdbqt file; no plugin required. To save the complex go to File -> Save Molecules... and then select the two entries and save.
Using a text editor (Don't use Notepad): If you have gedit or other Linux based text editors. Just open the docked ligand pdb file. Copy the coordinates and paste that at the beginning/end of the receptor pdb file or vice versa, using the text editor. Then open the file in PyMOL, it will show you the complex.
Rajiv Lakkaniga
how can i use maestro to combine the docking data and the PDB of the receptor.?
Just import both of them into the project table. Include both of them in the workspace. That's it.
But I guess Maestro can't read .pdbqt format which is default in Autodock. So, when you run a docking job in Autodock, make sure you export the results in .pdb format, not .pdbqt
1. Open vina result file in pymol.
2. Open ur pdb file of protein too. Now both receptor and docked ligand are in same window.
3 go to file, export molecule. Click save as pdb where u want. This is the pdb file of both receptor and ligand together
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