ADL: Protonating Macromolecule / Docking at Different pH

Joey Farrell jpfarrell at
Tue Sep 8 19:33:40 PDT 2020

Hi all,

I was wondering if there are any recommendations as to how to go about running a docking simulation using AutoDockTools and Autodock Vina at various pH levels. One potentially useful resource I found was H++, which evidently has automated pK calculation and corresponding charging/protonation, but I am not sure if there are other tools better suited for the task. Furthermore, in this case, should the application of Kollman/Gasteiger charges be skipped?

I would appreciate any insight on running docking simulations using this suite of tools at different pH levels.

Thank you in advance!


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