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I have been calculating the binding Affinity between a Ligand and a Protein using both AutoDock Vina and AutoDock tools but the binding affinity estimates obtained from the 2 molecular docking softwares are very dissimilar. For instance, in the example below the binding affinity estimated by AutoDock Vina is -12.6 but for the same Ligand and Protein the Binding Affinity according to AutoDock Tools is +158.0. Why would there be such a massive difference. Thank youenter image description here

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    $\begingroup$ You also scored a 2.11 kcal/mol in ligand efficiency, which is too good to believe as around 2.1 is the theoretical max! The autodock vina score has the correct sign and size, whereas the ADT looks more like a Ki value. I am not sure what is happening, but a good place to start is by looking at the dlg file and have a look there —there are lots of boring bits, but if you search for "lamarckian" or "____" (which is a table) you get to the fun stuff. $\endgroup$ – Matteo Ferla Oct 28 '20 at 17:58
  • $\begingroup$ @MatteoFerla I added the table from the dlg file. How do I determine the which value ADT has calculated. Is there anyway to find out if the ADT value is the Ki value. Thank you. $\endgroup$ – ibio_rep1 Oct 28 '20 at 18:55
  • $\begingroup$ Your RMSD are 70 Å: this is a lot. most protein are 20-30 Å in width. -800 kcal/mol is released by TNT, so those scores are really bad. My guess is that one or two files changed. Have you touched the map files between Vina and ADT? $\endgroup$ – Matteo Ferla Oct 28 '20 at 19:04
  • $\begingroup$ @MatteoFerla I haven't changed the map files. The binding affinity estimated for other Ligand Protein combinations by AutoDock Tools and AutoDock Vina are alike but for 2 Proteins i.e. Methyltransferase and Exoribonulease the binding affinty estimated by the two softwares is discrepant. $\endgroup$ – ibio_rep1 Oct 28 '20 at 20:26

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