[Chimera-users] problem with structure minimization

Elaine Meng meng at cgl.ucsf.edu
Fri May 18 10:39:01 PDT 2007

Hi Yunierkis,
Sorry - currently Minimize Structure does not work when a monatomic ion  
is present.  We would like to improve the behavior in the future.   
However, for now, if the bad contacts you want to fix are not that  
close to the active site, I would probably use the following procedure:  
  make sure the original structure is saved, add hydrogens and charges,  
delete the Mg++, minimize with the active site atoms frozen (make them  
the "Fixed atoms" during minimization), save another PDB, then  
text-edit the Mg++ from the original structure back in.  It is a  
judgement call of how much of the structure should be frozen.  If the  
bad contacts are fairly localized, you may want to allow only those few  
residues to move.

Minimize Structure man page:

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 May 18, 2007, at 9:42 AM, Yunierkis Perez Castillo wrote:

> Hi all.
> I'm trying to use chimera in order remove bad contacts in my crystal
> structure using the Minimize Structure under Tools -> Structure  
> Editing.
> I have a Magnesium ion in the active site of my protein and I need to
> keep it for further calculations.
> When I attempt to minimize the structure I get the following message in
> the reply log:
> AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> (see reply log for Python traceback info)
> Dock Prep runs with no problems and I'm able to save the mol2 file in
> which everything is OK, including hydrogen atoms, charges and Mg atom
> type and charge.
> If I remove the Mg ion from the structure, then the minimization runs
> with no problems. I think it is a problem while assigning amber atom
> type for Mg,
> Can anybody help me????
> Thanks in advance for any help
> Yunierkis
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