Subject: CCL: Summary of Responses on MM comparison to experiment

From: "Todd J. Raeker" <[email-masked]>
Date: Thu, 29 Feb 1996 10:27:08 -0500 (EST)

Hello all,

A while back I asked about articles that evaluate a number of MM force field 
in comparison to experimental data.  Here is a summary of all the replies.  
Sorry it took so long, replies were still trickling in last week.

Regards.

Todd.

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From: Abby Parrill     [email-masked]              

Dr. Raeker,
  We have completed this type of forcefield comparison on several 
carbohydrate derivatives.  The results were presented this fall in the 
first electronic glycoscience conference and are available at
http://mercury.aichem.arizona.edu/abby.html
by selecting the "Electronic Glycoscience Conference 1 Paper" link.  This 
paper has been accepted with revision to Glycoscience Journal.

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From: Per-Ola Norrby    [email-masked] (Per-Ola Norrby)

        Dear Todd,

        We recently completed a fairly thorough conformational
energy/rotation barrier study for 14 different force fields, for 40+
different organic compounds (most of the published cases for which accurate
potential energy / enthalpy data in the gas phase is available, plus some
:-).  The study is in press in J.Comp.Chem., it should appear in
March/April.  A previous version of this study, for some older force fields
as well as some semiempirical methods, has been published, "K. Gundertofte,
J. Palm, I. Pettersson, A. Stamvik, J. Comput. Chem. 12, 200 (1991)".

        If you are in a hurry, I could send you the text version of the
paper by Email.  To summarize: most MM2/MM3-based force fields (including
MM2(85) from the previous study), and the new MMFF from Tom Halgren, gave
good results (average errors below 1 kcal/mol).  Amber* is slightly worse,
but also gets in below the 1 kcal/mol limit in accuracy.  Most others gave
much worse results.  CFF91 is a special case.  It picks bad parameters
automatically, and therefore got a bad average, but for the systems where
it had well-determined parameters, it was among the very best.  Good but
risky!

        Regards,

        PeO
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From:  Benzion (Fuchs) [email-masked] Thu Feb 15 07:09:58 1996

Hi Todd,

Here are some references from our work on stereoelectronics
and crown ethers (there will be more soon):

Tetrahedron Lett. 1995, '36', 9193.
Tetrahedron, 1994 '50', 9691, 9707 and previous refs. cited there.

Regards,

Benzion (Fuchs)
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From: Klaus Gundertofte 3206 <[email-masked]>

Have a look in 

1991:142342   Document No. 114:142342  A comparison of conformational
     energies calculated by molecular mechanics (MM2(85), Sybyl 5.1,
     Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods.
     Gundertofte, Klaus; Palm, Jonas; Pettersson, Ingrid;
     Stamvik, Anders (H. Lundbeck A/S, Copenhagen-Valby, DK-2500, Den.).
     J. Comput. Chem., 12(2), 200-8 (English) 1991.  CODEN: JCCHDD.
     ISSN: 0192-8651.  

Furthermore, in the March issue of J.Comp.Chem to be issued very soon, we have 
a paper updating the above and including a wider variety of MM force fields.

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From: "Gregor Fels" <[email-masked]>

Todd,

there are a few articles on this topic in the "Reviews in Comp. 
Chemistry" series, e.g.
Vol 2, p. 81 - 97, 1991: J.P. Bowen and N.L. Allinger, Molecular 
Mechanics: The Art and Science of Parametrization
Vol. 6, p73 - 148, 1995: C.R. Landis, D. M. Root, T. Cleveland, 
Molecular Mechanics Force Field for Modeling Inorganic and 
Organometallic Compounds

By the way you can look up the articles of that series at
http://chem.iupui.edu/~boyd/rcc.html#home1.

As I am looking myself for articles on molecular mechanics that I can 
use for teaching I would very much appreciate if you let me know the 
answers you get on your request.

Gregor
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From: Mark Shenderovich   [email-masked] Mon Feb 19 12:11:40 1996

Dear Todd,

There was an interesting discussion in late 80-th on performance of 
different MM force fields for peptides and proteins:

Rotrman et al., Journal of Biomolecular Structure & Dynamics, 1989, 7, 
pp. 391-419 & 421-453 (2 papers).

These papers were followed by a discussion between Kollman's and 
Scheraga's groups in the same journal (1991, 8, 1103-1111). Of course, all 
force field tested in these 
papers have been updated since that, but in my opinion the papers and the
following discussion are important methodologically.

Dr. Todd J. Raeker          |  Department of Chemistry
Theoretical Chemistry Group |  Kent State University
[email-masked]      |  Kent, OH 44242-0001
Phone (216)-672-2986        |