[Chimera-users] Fe/HEM charge
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
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...
More information about the Chimera-users