Subject: SUMMARY: Book/review articles on forcefields.

From: <[email-masked]>
Date: Tue, 7 Nov 1995 19:28:25 +0000 (GMT)

Hi everyone,

Sometime ago, I posed this question to the CCL:

>Hi,
>
>Does anyone out there know of a good book or review article on forcefields?
>In particular, my colleagues are interested in any articles which may aid
>in choosing the 'best' forcefield for a particular problem - if such a
>thing exists (I know it is rather subjective, but they would appreciate any
>leads).
>
>Thank you for your time.

Well here's the summary many of you asked for. Sorry its taken a while - I was
away/busy/etc.

*Thank you very much* to all those who responded (I'm sorry I didn't thank
you all at the time).

Regards,

Tosh.

======================================================================

Dear Tosh,

        We have recently finalized a study where we compared accuracies in
energetic calculations for several current force fields.  It will appear in
J.Comput.Chem. in december.  I think some of it also got inte one of the
recent volumes (6 or 7) of Rev. Comp. Chem.

        In short, the conclusions are: don't trust force fields that use
"general" parameters.  The best results were obtained with reasonably true
implementations of MM2 and MM3 (there are many around that call themselves
MM2 or some such, you shouldn't always believe it), and also MMFF94.  When
it did not guess parameters, CFF91 gave good results.  Among simple,
harmonic, diagonal force fields, Amber* was outstanding (we didn't test
true Amber).

        Sincerely,

        Per-Ola Norrby

 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
 *  Internet: [email-masked], [email-masked]

________________________________________

You can look into "Reviews in Computational Chemistry": (1991), pp.81-97;
 99-164;1-55; (1992) pp. 73-142.

 Good luck.

##############################################################################

Gregory V. Nikiforovich                                   Phone (314) 935-4677
Research Professor                                        Fax   (314) 935-4979
Center for Molecular Design                            E-mail address:
Washington University                                  [email-masked]
Lopata Hall, Box 1099
St.Louis, MO 63130

##############################################################################

________________________________________

I have been co-editing a book series called Reviews in Computational Chemistry.
Several volumes have tutorial type descriptions about force fields. The latest
one is focused on force fields for inorganics and organometallics by Clark
Landis in Volume 6. It has references to other chapters on the topic you seek.
The book is published by VCH Publishers Inc. Your library may have it.
Kenny Lipkowitz
________________________________________

best is:
@incollection{Lipkowitz:94,
  author =      "",
  title =       "",
  booktitle =   "Reviews in Computational Chemistry",
  publisher =   "VCH",
  volume =      "I - IV",
  editor =      "K. B. Lipkowitz and D. B. Boyd",
  pages =       "",
  year =        "1994",
  OPTnote =     "eb--, [email-masked]",
  OPTannote =   "SCI-book"
}

though it is actually 6 books.
available in many libraries round the globe
eb
(Erich Bornberg-Bauer)

_______________________________________

Tosh,

  We are in the process of evaluating and comparing several forcefields
for use on carbohydrates.  This work is currently being presented in the
First Electronic Glycoscience Conference and will be published in the
proceedings.  If the molecules are anything like carbohydrates, let me
know and I can send you all sorts of data.

                      Abby Parrill
                  Chemistry Department
      Artificial Intelligence in Chemistry Laboratory
                The University of Arizona
             [email-masked]

______________________________________

I have collected literature recommendations from the net
in http://www.amber.ucsf.edu/amber/ - follow 'info from the net'->
'net texts' to see the index.

Bill Ross

______________________________________

Tosh,

have a look at Burkert & Allinger "Molecular Mechanics", ACS Monograph 177,
1982.
More recent information can be found in Lipkowitz & Boyd "Reviews in
Computational
Chemistry", VCH, Vol. 2 (1991) and Vol. 6 (1995).

Herbert

Herbert Koeppen, PhD, Medicinal Chemistry Department,
Boehringer Ingelheim KG, D-55216 Ingelheim, Germany
phone: ++49-6132-776845, fax: ++49-6132-773418
e-mail: [email-masked]

_______________________________________

>Hi,
>
>Does anyone out there know of a good book or review article on forcefields?

        This is a BIG topic. Maybe some introductory text would help you. The
        best one I can recommend are the books (both small) by Fletcher and
	Powell.
        called "principles of Resrained minimization" and "principles of
        unrestrained minimization" respectively. Its a bit tough at first if
        you are not mathematically inclined. But it will give you a grounding
        in the principles that will serve you well IMHO.
>In particular, my colleagues are interested in any articles which may aid
>in choosing the 'best' forcefield for a particular problem - if such a
>thing exists (I know it is rather subjective, but they would appreciate any
>leads).

        I would look for all of the force field validation experiments that have        been done. There are really not that many and I could give you some lead        references if you like. The KEY here is to find validations that are
        CLOSE to what you want to use the force field for. Even proteins
	(I'm just
        making an assumption here based on your address.) differ from one
	another
        and the various force fields may also vary in their ability to
	reproduce/
        "predict" the microstructure of the proteins.
>Thank you for your time.
>Regards,

All views expressed here are only my own.

Adi M Treasurywala Allelix Biopharma., 6850 Goreway Drive,
Mississauga, Ontario. CANADA L4V 1V7. (905)677-0831
FAX (905)677-5344

________________________________________

-- 
===============================================================================
 Asutosh T Yagnik,                           Tel: (+44) 1392 263451
 Protein Structure Group,		     Fax: (+44) 1392 263434
 Department of Chemistry,                    Email: [email-masked]
 University of Exeter,                 *  *  WWW: http://www.exeter.ac.uk/
 Stocker Road, Exeter. EX4 4QD. UK.      >                   ~ATYagnik/ATYagnik
                                       \__/      {All opinions are my own!}

 "Nature can provide for the needs of people, but not the greeds" M.K.Gandhi
===============================================================================