saving PDB files of complexes in Autodock
How can I save the PDB structure of protein-ligand complex (with single desired mode of ligand) in Autodock vina element?
And if I want multiple ligands within a single PDB, how to achieve that?
Dear @sudhir ,
If you want to save the whole document, in the latest version of SAMSON, you go to Home > Save or just press Ctrl + S, then you choose the PDB format.
If you want to save only some molecules, you select them, and in the latest version of SAMSON you use Selection > Save selection as.
I would like to save protein with the best conformation of the ligand as a complex but I am not getting it as a normal complex in a single file. kindly help.
Hi Sudhir, could you please tell us what you mean by "complex"? Do you mean one pdb file? multiple pdb files? In the results of AutoDock, you can activate a docking conformation by double-clicking it. Then, you select the structural models you want to save (e.g. the protein and the ligand), and you use Selection > Save selection as.
@admin one pdb file having protein and ligand docked.