[MMTK] energy minimizing a small molecule

Robert Jorissen robjorissen at yahoo.com.au
Fri Sep 26 23:20:40 UTC 2008

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

--- On Thu, 25/9/08, Konrad Hinsen <hinsen at cnrs-orleans.fr> wrote:

> From: Konrad Hinsen <hinsen at cnrs-orleans.fr>
> Subject: Re: [MMTK] energy minimizing a small molecule
> To: "Robert Jorissen" <robjorissen at yahoo.com.au>
> Cc: mmtk at starship.python.net
> Received: Thursday, 25 September, 2008, 4:30 PM
> On 24.09.2008, at 03:54, Robert Jorissen wrote:
> > However, this approach has not worked for other
> molecules. If I  
> > make copies of the heme PDB file and the heme
> Database/Molecules  
> > entry, and only change the PDB name from
> "HEM" to "HHH", and run  
> > the modified Python script, I get the following error
> message:
> The problem is that MMTK has no way to know that
> "HHH" refers to the  
> molecule defined by your new entry in Database/Molecules.
> It knows  
> for heme because the relation "HEM" ->
> Molecules/heme is hardwired  
> into MMTK. To tell MMTK about your new molecule and its PDB
> code, you  
> need to add
> 	from MMTK.PDB import defineMolecule
> 	defineMolecule('HHH', 'my_copy_of_heme')
> to your script before you do createMolecules(). If you
> don't, MMTK  
> will create an AtomCluster instead of a Molecule. An
> AtomCluster does  
> not have any force field parameters associated with it, so
> you can't  
> do energy calculations, as you found out.
> > And is the approach I used even the best way to read
> in a small  
> > molecule using MMTK?
> This is one of the two good ways to procede. The other one
> uses the  
> MoleculeFactory class to set up a molecule in Python code.
> > Also, I do not see a provision for adding improper
> angles. Are  
> > these automatically generated in MMTK?
> Yes, as are proper dihedrals and bond angles.
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> ---------------------------------------------------------------------

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