ADL: metal ion docking

Stefano Forli forli at
Mon Aug 13 11:38:32 PDT 2012

Hi Nidhi,

basically, you can find the most likely binding location of any cation by looking at the 
best energy of the postive potential (i.e. the absolute highest positive value) of the 
electrostatic map calculated by AutoDock.

The inhibition, on the other hand, is a totally different issue, and I don't know if it is 
possible to predict it upon a simple ion binding...


On 08/07/2012 09:36 PM, Nidhi Mathur wrote:
> Dear Sir/ Ma'am I am new to autodock. I would like to dock a metal ion say
> Mg with protein. i dont know how to prepare Mg ion as ligand. Also tell me
> if there is any way to find whether binding of Magnesium with protein will
> be sufficient to inhibit it or not.
>    Nidhi Mathur
> Lecturer-AIB
> 07742477500
> nmathur at
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> Amity University - India's No 1 ranked non-profit pvt University
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  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
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  The Scripps Research Institute
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