I have started a docking study with 3t4p using AutoDock vina in UCSF chimera. The DWSI inhibitor interacts with residues such as Lys 51, Asn 82, Thr 83, and Ser 80. After redocking, DWSI interacted with Lys 50, Asn 81, Thr 82, and Ser 79. These are not the correct residues to be reported. How do I fix this?
Hi Aaron Boakye
can't help but notice that you put "Lying" in one of your tags when it is not necessary. Best to put your frustration aside and hopefully you will see a clearer picture for your problem.Anyways, I'm assuming your 3t4p structure is from PDB so you need to understand that most of the structures is not complete (it has missing residues) and so does your 3t4p. I took a brief look and it is missing M on its' N terminal and several others on its' C-terminal thus prompting the different in residues number you are getting.
Secondly, docking results mostly dependent on the number of iterations you make especially so for AutoDock and AutoDockVina. You might get better results if you increase your run number.
All the best.
Is there any particular reason for using UCSF chimera????
I recommend to use PyRx or do the docking in Autodocktools (MGL tools)
Regards
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