[MMTK] adding pdb file to universe

Konrad Hinsen research at khinsen.fastmail.net
Thu Feb 2 08:49:18 UTC 2012

Ivan Vyalov writes:

 > I'd like to read PDB file with configuration of my system and then
 > to treat it by means of MMTK. To achieve this, as far as I
 > understand, one should read the PDB file and create MMTK objects
 > which then must be passed to universe.  However, I have encountered


 > the following problem: MMTK does not recognize atom types when I
 > want to create a universe from PDB. Another option is that I'm
 > completely missing something. Could someone help me with an advice?

The PDB format is particularly difficult to handle well, because
hardly anyone (not even the PDB) respects all the rules to the letter.
Your file for fluorine deviates from the PDB format in several places,
so it needs some work.

Concerning your script, there is nothing wrong with it in principle,
but since you have non-standard residues in your PDB file (the standard
ones are just biomolecules and water), you need to use

    config.createAll(permit_undefined = True)

The attached modified versions of your file work, so you can use them
as a starting point for further exploration. However, in your place I
would first think about whether you need PDB files at all. Your system
is very simple, and not at all biomolecular, so PDB may be more
trouble than it's worth.

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: research AT khinsen DOT fastmail DOT net
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