[Chimera-users] add atom type in MMTK

[Elaine Meng]

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:  
http://amber.scripps.edu/antechamber/tips.html
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  
compounds.

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


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
>