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Docking with auto dock vina

In the name of God. Docking with auto dock vina. Saleh Rakhshani Ligand: SAHA Receptor:HDAC8. HDAC8.pdb. Viewerlite. file>open>[select HDAC8.pdb]. open. Select HDAC8.pdb. Window>Hierarchy window. Hierarchy window. Remove all and keep active site. Remove. Keep. Remove. Ligand.

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Docking with auto dock vina

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  1. In the name of God Docking with auto dock vina SalehRakhshani Ligand: SAHA Receptor:HDAC8

  2. HDAC8.pdb

  3. Viewerlite

  4. file>open>[select HDAC8.pdb]

  5. open

  6. Select HDAC8.pdb

  7. Window>Hierarchy window

  8. Hierarchy window

  9. Remove all and keep active site

  10. Remove Keep Remove

  11. Ligand

  12. Remove default ligand

  13. Close and save…

  14. Save: yes to all

  15. Save to HDAC81.pdb

  16. Run Auto dock tools

  17. File>read molecule>[select]

  18. Edit>Hydrogen>add

  19. Select polar only

  20. Edit> Bond> addEdit> Charge> gasteiger • Show this message

  21. Grid> select molecule> choose

  22. Show this message

  23. Save pdbqt

  24. Grid> Grid box> save the numbers

  25. Ligand > input

  26. Ligand > torsion > torsion tree

  27. Choose torsion bonds

  28. Press Done

  29. Write a conf.txt

  30. Run auto dock vina

  31. Thanks

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