[chimera-dev] Following on new atom types (again)

[Eric Pettersen]

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 at 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?

--Eric

> 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 at qf.uab.cat
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