Subject: What molecular modeling means

From: Gregory Nikiforovich <[email-masked]>
Date: Fri, 26 Aug 1994 08:39:51 -0500 (CDT)

As any model, the model of a molecule you want to construct, is an image of
 a real molecule. You cannot build a model, which would account fot ALL
 properties of your molecule. Therefore, in any case, you will have to choose,
 which properties of the molecule you need most in THIS PARTICULAR CASE.

 If you need just to look at the connectivities, molecular graphics (or just
 image on the screen) would be fine. If you need to solve any conformational
 problems based on intramolecular energy values, you need to include intra-
 molecular interactions in your model at the level of atom-atom interactions.
 If you need to tackle any problem of covalent bond broking, you cannot
 escape quantum chemistry. And so on.

 The basic conclusion is, then, as follows: your model (and your software)
 should be chosen according to your problem, but not vice versa. The first
 approach is science; the second one is like looking for a lost item just 
 under a street light, but not in the dark street, where it was lost. Well,
 sometimes it was lost in the right place...

 Gregory Nikiforovich
 Research Professor, CMD, WU at St. Louis.