[MMTK] energy minimizing a small molecule

Guido Wagner wagner at chemie.uni-frankfurt.de
Sat Sep 27 10:36:05 UTC 2008

Hi Robert,

the examples are in the Examples/Miscellaneous directory:

molecule_factory.py and read_xml.py

The XML-molecule factory class is in MMTK/XML.py

I have MMTK 2.5.18

There is no support for the attribute "amber_atomtype" yet, so you will 
have to add this yourself. This is only a few lines of extra code: Just 
stick to the lines that handel "elementType".

On the homepage of the cElementTree Module 
(http://effbot.org/zone/celementtree.htm) they have good tutorials on 
how to use it to read an manipulate XML files.



Robert Jorissen schrieb:
> Thank you to Guido and Konrad for your replies.
> With Konrad's two extra lines of code, I able to read in and minimize my heme molecule. Likewise, I could read in and minimize a benzene molecule (I had created an appropriate database entry.)
> I would like to know more about the MMTK XML-molecule-factory. I am unable to find an appropriate example. It seems that there used to be one, but I am unable to find one.
> Rob Jorissen
> Ludwig Institute for Cancer Research, Melbourne branch

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