[MMTK] modeling arbitrary structures

Konrad Hinsen hinsen@cnrs-orleans.fr
Tue, 7 Aug 2001 20:59:00 +0200


> PyMOL has a minimalist molecular representation -- essentially PDB
> records with the following additional properties for purposes of
> modeling:

PDB records have one problem - they assume a "chains of residues"
representation. Which is fine for polymeric molecules, useable for a
bunch of very simple molecules (e.g. water), but not very convenient
for anything in between.

I wish we had some better data exchange format than PDB, preferrably
XML-based.

> Assigning MMFF atom types is quite trivial (just pattern perception),
> but doing the same for Amber would be quite a challenge.  Although I've

Indeed.

> 	Furthermore, I question whether a simplistic forcefield such as
> Amber (just bonds, angles, torsions, impropers, and pairwise nonbonded
> potentials) is sufficient to capture dynamics (or even geometry) of
> small molecules in a general sense.  At the very least, to do this right

Good question, some people think it does, others think it doesn't. We
won't know until someone has tried it. But that someone won't be me!

> you would basically need to start from scratch with a new set of generic
> atom types for small molecules and develop "compromise" parameters for
> these atom types.  That is a Ph.D. thesis sized project, not something
> one could cook up on a weekend...

Of course. On the other hand, implementing a more complicated force
field such as MMFF is also more than a weekend's job. In principle
everything is clear, but getting all those additional terms and their
derivatives right, plus testing everything, is a lot of work.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------