ADL: How to consider Heme iron as Fe3+

Laura Furge Laura.Furge at
Mon Jun 17 03:57:44 PDT 2013

You open the PDB coordinates file in a text editor; the iron atom is at
the bottom of the atom list. Go to the "charge" column and change to 3.
Resave file.

I'm curious what responses you will get because we have always been told
for docking to keep the iron at zero (told this by both Eric Johnson's
group at Scripps and by a molecular dynamics/modeling group at Pfizer in
LaJolla). So, if you hear anything interesting in response to your post,
would you mind sharing with me?

Laura Lowe Furge, Ph.D.
Professor & Chair of Chemistry
Kalamazoo College
1200 Academy Street
Kalamazoo, MI 49006
email: Laura.Furge at
FAX: 269-337-7508
Phone: 269-337-7020

On 6/17/13 6:38 AM, "Hamid Irannejad" <irannejadhamid at> wrote:

>Dear Colleages
>As you know, iron atom in Heme has 3+ charge but in preparing pdbqt file
>protein with AutoDockTools, the iron atom becomes zero charge !!!
>How can I modify or change the charge of iron atom???
>--- ADL: AutoDock List  --- ---

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