ADL: Unsuccesful redocking

Leo Juhlin leojuhlin at gmail.com
Mon Apr 13 05:51:24 PDT 2020


I tried to redock a ligand into a known crystal structure. Even though I
used the same protein as from the crystallized structure I still get the
highest ranked pose with an carboxy group pointing in the opposite
direction in comparison the crystallized ligand, as can be seen in the
linked picture below. I´ve run the docking multiple times both in vina and
autodock4 but still get this pose.


https://imgur.com/qZx8N7A

It doesn´t make sense to get this pose since the carboxy group of the true
ligand pose is hydrogen-bonding with a positively charged lysine side chain
nitrogen.

Could anyone give me some advice why I won´t get the right pose?

Best regards, Leo


More information about the autodock mailing list