Now, I am working do dock some molecules using the Auto dock but one of ligands gave a positive binding energy so I suggest that there is no interaction between the ligand and the protein But I tried to dock the same ligand with the same protein using PyRx auto dock vina the obtained binding affinity is negative and the discovery studio 2D interaction diagram showed that the ligand bind to the active site?
So why the auto dock gave no interaction (+ve binding energy) or there is something I have to do?
check your protein preparation when docking with autodock...Also probably the config file contains errors in the receptors name
Check your protein structure as well as ligand structure.. I think they are not in the energy minimized state. Redock with proper structure.
Make sure that your structures are energy minimsed and you have added the charges( kollman for protein, Gasteiger for Ligand) if you fail to do minimisation or add charges then AutoDock 4.2 cannot detect the interactions and you may get wrong results. Vina is more accurate and faster than Autodocm as it calculates parameters internally. In AutoDock 4.2 you have to do these your own. So if you fail to do it, you may get wrong results.
Thanks for your helpful answers,
The ligand and the protein structures were energy minimized but the problem still present.
Can any one suggest a good server for protein energy minimization?
Hello Vikram Dalal,
Thank you for detailed answer, I will try your suggestions
Regards
In general is important to prepare ligands and proteins before docking
this is very important step do in this way your results are good proof of binding energies
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