Subject: CCL:Molecular modeling software for non-theorists?

From: "Prof. Robert Shanks" <[email-masked]>
Date: Fri, 13 Jun 1997 8:34:01 EST-10ESUT

To:  Julius Su
Molecular modeling software for non-theorists?

We use:
Chem3D (Macintosh)
Hyperchem (MS Windows)
CAChe (Macintosh)
MSI Insight II Polymer (Silicon Graphics)
Unichem (Silicon Graphics interface, Cray computations)

I can reiterate your experience with Chem3D, in fact the Chem Office programs are well 
integrated and offer full scripting and web interaction.
Hyperchem is similar, but a stand alone modelling program. It has more display facility than 
Chem3D in that it can display orbitals. It can also compute vibrational modes. It has similar 
ease of use to Chem3D. 
CAChe has more extensive computations than either of the above and it is property based. 
On the Macintosh it has an automatic spreadsheet type entry system (Project Leader) for 
molecules and properties - once this has been setup the program will automatically move 
through all the properties desired for each molecule and place the values in the cells. It has 
some QSPR type computations in addition to the quantum mechanical and molecular 
mechanics methods.
MSI Insight we use onlt for polymers. It is a research tool which is not in the same category 
as the above programs.
Unichem is a quantum mechanics program. It is only difficult to use in that it requires links 
with a Cray Supercomputer.

Sincerely
Robert Shanks

From:          [email-masked] (Julius Su)
Subject:       CCL:Molecular modeling software for non-theorists?
To:            [email-masked]
Date:          Mon, 9 Jun 1997 21:40:42 -0700 (PDT)

Hello,

  I work for a research group that uses laser spectroscopy to investigate
the basic dynamics of chemical systems on a short time scale.  Some 
members of our group have done fairly high level ab initio and molecular
dynamics simulations in the past; however, the main focus of the group
has definitely been experimental.  

  Because of this, there has been no standard way to model chemical
systems in our group.  Individuals in the group have either written
their own molecular dynamics routines or have had access to facilities
where programs like Gaussian 92 could be run, but no convenient in-group
facility to do simple molecular modeling has existed.          

  We are currently seeking to change this.  We would like to have some
standard way of finding the geometries of small to medium molecules
at a reasonable level of theory (semiemperical would be fine) and
for doing molecular dynamics of photoexcited systems.  This system
would have to be accessible and easy enough to use that any experimentalist
that wished to carry out an experiment would be able to quickly
throw together a rough simulation of the system in question.

  Our group plans to purchase two fairly high end PCs to run the
software that would be needed to do this.  I have recently purchased a
copy of Chem3D Pro with MOPAC for my personal use, and have found the
interface for molecule building and geometry optimization to be
intuitive and easy to use.  We also have some simple code that was
written within the group to do molecular dynamics on small clusters
of rigid molecules.  This code can be easily interfaced with Chem3D.

  Alternatively, we have found information on the Web about HyperChem,
which appears to have the ability to do model building, geometry optimization,
and a feature that would be especially useful to us, reactive molecular
dynamics.  It also appears to have facilities built in to visualize
vibrational modes and molecular oribtals (althought the latter feature
would not be nearly as important.)  Since our group already has a copy
of Gaussian 94, the added ab initio capabilities of the program are
nice but not essential.

  The main concern at this point, however, is how easy HyperChem would be 
to use.  Chem3D has impressed us with its intuitive interface and its
tight integration with ChemDraw.  We have not been able to find a 
demo of version of HyperChem with enabled building facilities to 
compare.  Since 90% of the time will probably be spent doing simple
model building and geometry optimization, this is particularly      
important to us.

  So, has anyone on this list had experience with HyperChem and Chem3D?
How easy is it to build molecules in HyperChem?  Does it have a 
reasonably useable interface?  Can it generate publication quality
graphics?  Can experimentalists who don't want to spend too much
time learning the nitty-gritty of semiemperical theory do simple
calculations using it?

  Thank you very much for your help.

Later,

Julius Su
[email-masked] 

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__________________________________
Prof. Robert A. Shanks
Professor of Polymer Science
Department of Applied Chemistry
Royal Melbourne Institute of Technology
Box 2476V GPO
Melbourne Victoria 3001
Australia
Telephone and Fax +61 3 6602122
Mobile Telephone +61 041 935 8001
WWW RMIT Polymer Science Page:
http://www.rmit.edu.au/departments/cm/polymer/index.html
__________________________________