[Chimera-users] heme (fe) containing enzyme

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 17 09:07:42 PDT 2009

Hi Agus,
The Minimize Structure tool is currently rather limited. Unfortunately  
only the following monatomic ions can be handled: Na+, K+, Rb+, Cs+,  
Mg2+, Ca2+, Zn2+, and Cl–.

The workaround for the ion problem is to change FE to ZN (for  
example), but freeze the ion and nearby residues so that this change  
does not affect the structure.  You would do that by selecting a zone  
around the ion (Ctrl-click it and then use "Select... Zone..." in the  
menu) and specifying "Fixed atoms: selected" in the Minimize Structure  
tool.  Of course, then that part of the structure won't be adjusted.   
Ways to change FE to another element are: text-editing the PDB file,  
or using the Modify Atom section of Build Structure (under Tools...  
Structure Editing), or using a command something like:

setattr a element Zn Fe

I don't know what is happening with your histidine.  If you still get  
that problem use "Help... Report a Bug" in the Chimera menu, and  
include information such as what structure you are working with and  
what led up to the error (and your e-mail address if you want a  
further response after the bug report).

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 Mar 17, 2009, at 1:19 AM, Agus Setiawan wrote:

> Hi, I'm a student of Pharmacy and I just learn about chimera.
> Actually, I want to run a docking using Autodock so I have to  
> minimze the structure of macromolecule first. I choose Chimera to  
> minimize the structure of macromolecule. However, there is an error  
> because the Fe atom doesn't have GAFF
> "Unable to find GAFF type for #0:500.A at FE"
> I also have a problem with hydrogen at Histidin residu
> "no MMTK name for H at standard HIS"
> How can Isolve this problem?
> I'll be very thankful for your answers.
> Best Regards,
> Agus Lee.

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