I did molecular docking in Autodock vina. I have seven different confirmations. But I want to know how we can build a complex in order to know the ligand interactions.
Dear Renjith,
Seven different confirmation means seven different binding pockets of your ligand in protein. You have to choose the best confirmation and then select the binding site residues of your protein which are generally surround the ligand. After this, click on A on PyMol and select show interaction. Once you click, the interaction between ligand and residues of protein will generate.
Dear Renjith,
You can visualize, analyze and create pdb files using Autodocktools. You can find attached a tutorial.
All the best.
Miguel
http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
You can drag both Receptor and ligand .pdbqt files into the openBabel software and convert them into a file (pdb, sdf ,..). Check the Center coordinates box for generation connection and coordinations in the resulted file.
In the case of PDB files you can open both receptor and ligand files with UCSF Chimera and safe both file as a complex in a single .pdb file.
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