[Chimera-users] add atom type in MMTK

Elaine Meng meng at cgl.ucsf.edu
Fri May 30 17:34:49 PDT 2008

Hello Lionel,
Are you trying to run "addcharge" or "minimize"?

If "addcharge" to calculate partial charges on some Pt complex (e.g.  
cisplatin or carboplatin):

Nonstandard residues are sent to Antechamber, but that program is  
only meant to be used on organic molecules (C,H,O,N,S,P,F,Cl,Br,I),  
not metal complexes or inorganic species.  See the antechamber site:  
I think you have to use some other program that can handle metal  
complexes to derive partial charges.  I don't think it is possible to  
simply edit some antechamber data files to get it to work on such  

If "minimize" and you just wanted to treat the Pt as a monatomic ion  
with integer charge:

I had thought it possible to add a metal ion type by editing a  
parameter file.  However, I have not been successful at minimizing a  
structure with the "new" type even when the file appears to include  
the necessary parameters.  Maybe there is an additional step that I  
don't know about.  So currently my best answer is that it is not  
possible, but if we find a way, we will send another message. (I may  
be wrong given my lack of success, but I think the relevant parameter  
file within the Chimera installation is lib/python2.5/site-packages/ 
MMTK/ForceFields/amber/amber_parm99 )

Sorry about that,
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 30, 2008, at 5:52 AM, Lionel Nauton wrote:

> hello everybody
> this is my first question since I use chimera, more than 3 years ago,
> and I would like to know
> if is it possible to add atom type in the MMTK basis set ?
> I actually work on a molecule containing platinium, and I can't run  
> mopac
> because there is no description.
> I'm looking for some description files , and I found this :
> /antechamber/dat/antechamber/*****.DAT
> which is the good one and which is the way to modify it ?
> thank's for your answer and excuse me for my english.....
> best regards

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