I was doing blink docking using AutoDock Vina. All the parameters are same, ligand and receptor also the same, just that the grid box center is a little bit different (I did at different time frame, so I set the grid box twice with autodock tools). By principle, isnt it both the results should be the same, since the grid box have covered the whole receptor. Can any one explain why I get different results? And which one should I take?
Chong Qi In theory, you could have several poses energetically similar and the program will give you a different pose each time. You could perform several runs and see if certain poses appear more often than others. We proposed a way to perform these blind dockings and have an idea of what the program is doing and why it is picking certain poses. Have a look here:
https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki/4.2.4-Automatic-mode-using-AutoDock-Vina
hope this helps!
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