[Chimera-users] Fe/HEM charge

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 4 11:45:49 PDT 2007

To follow up to Elaine's reply, Antechamber does not handle metals  
well.  I will try to get Chimera to notice when a residue is a metal- 
coordination complex and ask for the metal/non-metal formal charges  
separately, and only send the non-metal part off to Antechamber.  So  
for now Elaine's suggestion of temporarily deleting the metal is  
probably the best workaround.

On top of this problem, there is a bug in Antechamber where it  
identifies the iron as fluorine, since it only treats atom names that  
start with 'Fe' as iron (not 'FE'!).  Since Antechamber determines  
the number of electrons by adding up the atomic numbers + formal  
charge, that's why it is only working with odd formal charges (iron's  
atomic number is 26; fluorine's is 9).


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Jun 4, 2007, at 10:24 AM, Elaine Meng wrote:

> Hello,
> 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
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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