[MMTK] Re: The use of ions.

[Julien MOZZICONACCI]

Hi Konrad, thank you for your answer.
 
> > I'd like to know if someone has done something for ions.
> > Should I just add them to the database? Where? in molecules?
> > What name should I give to those files in ordrer to be able to recognize 
> > them in PDB files?
> 
> There are several options, but one-atom molecules are probable the
> best description. For the correct assignments to PDB residue names,
> see the documentation of the module MMTK.PDB.

That is what I am trying to do. In order to recognize my ion in a PDBfile, 
I thought that I sould use the createMolecules method of the 
PDBConfiguration Class.
In fact, a problem raised. I send to you this Traceback because I really 
don't know how to get rid of it.
 
Traceback (most recent call last):
  File "test_database.py", line 24, in ?
    universe.addObject(configuration.createMolecules(names = 'water'))
  File "/usr/lib/python2.2/site-packages/MMTK/PDB.py", line 220, in createMolecules
    if names is None or name in names or full_name in names:
TypeError: 'in <string>' requires character as left operand

I hope that you can help me.
Best regards.

Julien Mozziconacci.