Subject: ForceField:summary

From: Stanislav Ivan <[email-masked]>
Date: Fri, 17 Aug 2001 09:20:25 +0200

Dear CCL'ers,
thank you very much for your advices.Following is my former question and
all of replies.

Dear CCLers,

 I am PhD student and  I am just starting calculations using Force Field

 methods.
 Could you please advice/suggest me some basic references about Force
 Field with the description of basic methods (AMBER, MM2 etc.) and their

 preformance on different systems (proteins,DNA, general organic
 systems), reliability of such calculations, ....
 Thanks in advance.

Stanislav Ivan
Institut fur Organische Chemie
4056 Basel
Switzerland
[email-masked]

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Get the book by Andre Leach "Molecular Modelling" (Longman publishers)

--
Groeten, David.
________________________________________________________________________

Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry

Husargatan 3, Box 576,          75123 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
[email-masked]    [email-masked]   http://zorn.bmc.uu.se/~spoel

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I would recommend the following;

1. "Computational Chemistry; A practical guide to applying techniques
to real world problems. ", David Young, Wiley-Interscience, 2001

This is a new but very good book. A bit quantum focussed, but still
good.

2.  "Molecular Modeling: Principles and Applications", AR Leach, 1996,
Essex, Addison Wesley Longman Limited

        A much more robust book (595 pp) that goes into more detail than
Grant
and
Richards.  Gives more examples and a more solid theoretical foundation
for
the techniques.  My choice for a graduate level textbook.

3.  "Dynamics of Proteins and Nucleic Acids," JA McCammon and SC Harvey,

1987, Cambridge, Cambridge University Press.

        Always a classic - an excellent (though a little dated)
description of
simulations of proteins and nucleic acids.  Good low level introductions
to
theory with some nice examples and applications.

Dr. Shyam Vyas
Applications Scientist
Accelrys Inc.
(formerly Molecular Simulations Inc)
300 Lanidex Plaza, 3rd Floor
Parsippany, New Jersey 07054
Phone: 973-386-5549
Fax:    973-386-5584
Email: [email-masked]
Mobile: 1-201-738-4137

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Regarding your request for information on force fields, you might want
to check out Reviews in Computational Chemistry.  This book series has
had a number of chapters on force fields, molecular mechanics, and
simulations.  Two of these chapters are:

I. Pettersson and T. Liljefors, in Reviews in Computational Chemistry,
VCH, New York, 1996, Vol. 9, pp. 167-189.  Molecular Mechanics
Calculated
Conformational Energies of Organic Molecules:  A Comparison of Force
Fields.

M. Jalaie and K. B. Lipkowitz, in Reviews in Computational Chemistry,
Wiley-VCH, New York, 2000, Vol. 14, pp. 441-486.  Appendix:  Published
Force Field Parameters for Molecular Mechanics, Molecular Dynamics,
and Monte Carlo Simulations.

Donald B. Boyd, Ph.D.
Editor, Reviews in Computational Chemistry
        http://chem.iupui.edu/rcc/rcc.html
Gordon Research Conferences on Computational Chemistry
        http://chem.iupui.edu/rcc/grccc.html
Department of Chemistry
Indiana University-Purdue University at Indianapolis
Indianapolis, Indiana 46202-3274, U.S.A.
E-mail [email-masked]

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Two nice tutorials on the topic of force fields exist in Reviews in
Computational Chemistry, Volume 2, 1991, VCH Publishers (now Wiley-VCH).

Chapter 4: New Approaches to Empirical Force Fields by Dinur and Hagler
and
Chapter 3: Molecular Mechanics: The Art and Science of Parameterization
by
Bowen and Allinger.

An assessment of how well different force fields do for different types
of
problems has been reviewd in that book series (Volume 9, published in
1996) by
Peetterson and Liljefors. A fairly up to date listing of publications in
which
force field parameters have been published exists as an appendix in
Volume 14
(published by Wiley VCH in 2000).

There exist several stellar books on the topic of force fields as well
but
these aforementioned chapters are designed as tutorial-type reviews
which are
quick to read.

Lipkowitz
[email-masked]

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CHARMM22
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies
of Proteins
J. Phys. Chem. B 1998, 102, 3586-3616

OPLS
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins

 via Comparison with Accurate Quantum Chemical Calculations on Peptides
J. Phys. Chem. B 2001, 105, 6474-6487

Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for
Modeling Organic Liquids
J. Phys. Chem. 1996, 100, 18010-18013

Development and Testing of the OPLS All-Atom Force Field on
Conformational
Energetics and Properties of Organic Liquids
J. Am. Chem. Soc. 1996, 118, 11225-11236

Lic. Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica
Facultad de Ciencias Quimicas
Universidad Nacional de Cordoba
Ciudad Universitaria
(5000) Cordoba
Argentina

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Gundertofte et al., Journal of Computational Chemistry Vol 17 No 4,
429-49
(1996)

M.D. Beachy et al., Journal of the American Chemical Society, Vol. 119,
5908-5920 (1997)

--
Eric Bennett ( [email-masked] ; http://www.pobox.com/~ericb )

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You might read "Molecular Mechanics Across chemistry", by Rappe and
Casewit,
1997.

E. Lewars

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Study the book of Jensen (Introduction to Computational Chemistry),
or Leach (Molecular Modelling: Principles and Applications).

--
Marcel Swart

Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB)
Rijksuniversiteit Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

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