[MMTK] energy minimizing a small molecule

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Sep 25 16:30:51 UTC 2008

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 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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