saving PDB files of complexes in Autodock

  • Hello,
    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.

    For some particular ways of exporting structures into PDB files you can also use Export Along Paths Element (see the Export atoms trajectories along paths tutorial)

  • 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.

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