Molecular Modeling Requirements

The following steps are required to prepare your machine to be fully capable of first order molecular modeling. You should read through these requirements carefully. Unless you are a software expert, omitting even one step in the following procedure will cost you large amounts of time and money. If you exactly follow these steps, you will be up and running sophisticated software in no time.

First: Visit and Implement Hardware Requirements

Second: Molecular modeling means different things to different people. Definitions clarify.

Definition: "first order molecular modeling" means:

a) being able to display two dimensional ".gif" images of molecules
b) being able to interactively edit the structure of those molecules to produce different molecules
c) being able to save those edited structures to a file for later use
d) being able to look up the chemical name, CAS number and properties for that molecule using only the structure.

e) being able to display three dimensional ".mol" or ".pdb" renderings of molecules
f) being able to find minimum energy configurations for those molecules
g) being able to simulate the molecular dynamics of those molecules, i.e. vibrational modes

I have searched these matters out thoroughly. The most cost and time effective way of reaching these goals are:

0) download and install the Free MDL Chime Plug-in.
Test step 0 by visiting my site.
You should see molecules spinning on a black background in your browser.
If you don't AND ONLY if you don't, send me email.

1) purchase and install the $249/$299 academic version of the ChemDraw Pro program on CD.

READ THIS CAREFULLY OR YOU WILL WASTE 1 WEEK!

At the beginning of the CD installation
ChemDraw Pro will ask you which browsers you want to install plug-ins to.
Uncheck all boxes that correspond to web browsers.
DO NOT install THOSE plug-ins.
They BREAK the MDL Chime Plug-In.
Continue with the rest of the installation normally.

Test step 1 by visiting http://www.wdv.com/Biochemistry
The molecules should look the same as before, on a black background.
If they don't, something is wrong. Recovery may be possible. Stop and send me email.

2) download and install the Free ChemDraw Pro Plugin 5.0 only

This patches (solves) the MDL Chime breakage problem, and gives you a first class plug-in program.
The plug-in is free because it uses the serial numbers you got when you paid for ChemDraw Pro.
Test step 2 by visiting my site.
You should see molecules in your browser.
If you don't AND ONLY if you don't, send me email.

3) download and install $299 Chem3D Pro 5.0.

Install the standalone application.

Test step 3 by visiting my interactive NSAIDs simulation site.
You should seee 3D molecules slowly turning on a black background.
If you don't see AND ONLY if you don't, send me email.
If you click on the stoichiometric formulas, a 3D model of the molecule should fire up.
You can do minimum energy configurations and molecular dynamics with this tool.
Try editing and simulating more complex molecules such as Substance P.

If everything works at this point, you have achieved first order molecular modeling, on your desktop, without the cost or expense of "big iron" workstations.

L. Van Warren
Warren Design Vision

Last Updated 8/19/1999