[Chimera-users] Fe/HEM charge

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 4 10:24:55 PDT 2007

Yes, you can have Fe(II) in Chimera.  I am guessing that in your  
structure, the Fe ion is part of the residue named HEM. In this case  
(using PDB entry 1a6m as my example), addcharge fails if you set the  
net charge to an even number. The HEM residue in 1a6m is  
protoporphyrin IX and iron, where (I think) the protoporphyrin IX has  
a net charge of -4.  So if you wanted Fe(II), the net charge would be  
-2, which leads to an error message and Antechamber failure.

The problem is that what the PDB thinks is one residue is more  
appropriately treated as two separate residues for charge  
calculation.  Chimera tries to do everything for you and just treats  
each residue as a molecule, but in this case it should be two  
separate molecules.

I recommend editing the PDB file in a text editor to change the  
residue name of the Fe atom to something else so it will be perceived  
as a separate residue.  In the case of 1a6m, I changed the residue  
name of the Fe atom to FE2, re-opened the structure, added hydrogens,  
and then in the addcharge dialog, I used +2 as the formal charge of  
the FE2 residue and -4 as the formal charge of the HEM residue (the  
original HEM minus the FE atom).

Another possible approach would be to just delete the FE (after  
hydrogen addition so you don't get unwanted hydrogens on the  
porphyrin part), calculate charges, and then edit the FE atom back in  
to the resulting PDB file.  You could then put the +2 charge on the  
FE with the "setattr" command or just edit that charge into an output  
Mol2 file, if the purpose was to create such a file.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 4, 2007, at 5:08 AM, Газизов А.С. wrote:

> Hello everybody.
> Is there Fe2+ ion in Chimera? I'm trying to add charges to hem
> molecule and it always appears to be Fe3+ (and Add Charge tool
> reports "There is odd number of electrons..." and fails).Assigning
> odd overall charge helps (i.e. +1, +3, etc), but I need +2...

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