I'm using autodock vina for docking analysis.I successfully conduct docking procedure but failed to join receptor and ligand into one.I used pymol for this process.
What's the appropriate way to construct one file for ligand and receptor in pymol?
Should i use any other software for this part?
Thanks for your co-operation..
Dear Niloy Kumar,
Once you generate the vina output file (out.pdbqt) use vina_split.exe and run vina_split --input out.pdbqt command. Vina split generates separate .pdbqt files based on the ranking.
Now, you can open it in any text editor and copy everything at the bottom of your target file and save as a separate .pdb file.
Hope it helps..
Do you want to visualize their interaction? You can do that easily with autodock tools, without any other file operations.
To do this open autodock tools and follow this:
1. Analyze > Macromolecule > Open [select your receptor .pdbqt]
2. Analyze > Docking > Open Autodock Vina result [select your vina output .pdbqt]
Now from the left panel you can control how you want to see them. Like.. give sepearate color/appearance for protein and ligand.
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