On Mar 18, 2013, at 3:34 AM, Elisabeth Ortega wrote:

Dear Chimera dev. Team,

I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported".

This means that the platinum atom does not have a "gaffType" attribute assigned. This attribute should have been assigned by AddCharge. If you are assigning the charges yourself, you need to assign some gaffType to the platinum (I guess I suggest: setattr a gaffType Pt Pt).

As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens.

What does "nothing happens mean exactly? Does no minimization occur? Does a minimization occur but no atoms move?

Probably I'm modifying the wrong files...

Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it?

Thank you so much for your time and your patience.

--
Elisabeth Ortega Carrasco, Ph.D. Student
Molecular Modelling of Transition Metal Systems Group
Lab. C7/153, Chemistry Department
Universitat Autonoma de Barcelona

Tel.: +34935812857
email.: ortega.elisabeth@qf.uab.cat
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