[Chimera-users] problem with structure minimization

Yunierkis Perez Castillo Yunierkis at cbq.uclv.edu.cu
Fri May 18 09:42:31 PDT 2007

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


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