Subject: Summary /search for review papers on parameterization of force fields

From: <[email-masked]>
Date: Fri, 14 Jan 1994 13:56:42 -0500

Summary /search for review papers on parameterization of force fields

Many thanks to those who responded to my query. Here goes the summary.
Weigen Liang

original posting:
From:	SMTP%"[email-masked]" 11-JAN-1994 
Subj: search for review papers on parameterization of force fields

Dear netters,
  I'm searching recent literature for REVIEW papers of parameterization of 
force field in molecular modeling without much success. In some lucky cases I 
found papers reviewing a particular type of force field, i.e., MM3, DREDING, 
UFF, etc, but most of the time I just got papers dealing with a small series 
of molecules, even a single molecule. 
  Does anybody have a good lead to those papers which review (or invent)  
particular types of force fields, even the whole field of parameterization 
of force field in molecular modeling? I would appreciate it if you give me 
a clue, and if there are significant emails, I'll summarize them and post 
them to the list. 
Thanks.
Weigen Liang

Responses from dear netters

ff-1
From:	SMTP%"[email-masked]" 11-JAN-1994 12:37:06.74
Joerg-R. Hill

Look at:
1) The Consistent Force Field and Its Quantum Mechanical Extension, A. Warshel
   in: Semiempirical Methods of Electronic Structure Calculation, Part A:
   Techniques, (Modern Theoretical Chemistry 7), Ed. Gerald A. Segal, Plenum
   Press, New York and London, 1977, p. 133
2) Molecular Mechanics Force-Field Parameterization Procedures; A. J. Hopfinger,
   R. A. Pearlstein, J. Comp. Chem., 5 (1984) 486 - 499
3) Proximity effects on organic reactivity: Development of force fields from
   quantum chemical calculations, and applications to the study of organic
   reaction rates; Andrea E. Dorigo, K. N. Houk in: Advances in Molecular
   Modeling, vol. 1, JAI Press Inc., 1988, p. 135
4) Derivation of force fields for molecular mechanics and dynamics from ab
   initio energy surfaces; J. R. Maple, U. Dinur, A. T. Hagler, Proc. Natl.
   Acad. Sci. USA, 85 (1988) 5350
5) J. R. Maple, T. S. Thatcher, U. Dinur, A. T. Hagler; Chemical Design
   Automation News 5, 9 (1990) 10

ff-2
From:	SMTP%"[email-masked]" 11-JAN-1994 12:40:18.33
Peter S. Shenkin

Well, you could go to the original AMBER, MM2, MM3 or OPLSA papers.

Also, there's still good stuff in Burkert & Allinger, "Molecular
Mechanics" (ACS Monograph 177), which would be a good place to start.

ff-3
From:	SMTP%"[email-masked]" 11-JAN-1994 13:37:34.38
Chan-Kyung Kim

    Prof. Wolfe published series of papers in the Canadian Journal of Chemistry,
66, 2687 - 2750 (1988). In these papers, he developed MMP2 parameters for 
peptides and penicillins.

ff-4
From:	SMTP%"[email-masked]" 11-JAN-1994 13:46:58.75
Max Vasquez

        The november 93 issue (No. 7) of Chemical Reviews is dedicated to
molecular mechanics and modeling.  Unfortunately, Arnie Hagler's contribution
did not make it in time for that issue: it was(is) a review of current force
field methodology.  Still you may find some of the other articles quite
useful.  Also, there are two recent papers in JACS "inventing" new force
fields, and at the same time presenting a brief overview (not really a
review) of other force fields (at least the major references are given).
These are:
(1) Amodeo & Barone JACS 114, 9085-9093 (1992)
(2) Halgren JACS 114, 7827-7843 (1992)

Attempts to compare force fields seem to run into controversy; see for example
the discussion in J.Biomol.Struct.Dynamics 8, 1103-1111 (1991) between 
Kollman's and Scheraga's groups regarding force fields for biomolecules.

I hope this helps.  In any case, keep you eyes open for Hagler's paper in
Chem.Rev. to appear sometime soon.

ff-5
From:	SMTP%"[email-masked]" 11-JAN-1994 15:58:13.71
Tudor-Ionel Oprea

one of such paper series, but without comprehensive examples,
is generated by JG Vinter and colleagues, concerning the 
COSMIC force field and molecular modelling package.
Three papers i have in mind, all published in JCAMD,
Vinter et al, JCAMD 1:31-51 - about COSMIC
Abraham, Haworth JCAMD 2:125-135 - about the Morse potential
Morley et al, JCAMD 5:475-504 - about COSMIC(90)

these papers reflect the evolution of a good force field
(as compared to others), that is based on a simple philosophy:
keep atom types to a minimum (only 26 at types)
compare that with 200 for CHARMm and ilk
(bare in mind it is a general organic ff, so metals should
be not counted)

Enjoy the papers - most of the times you will find that they
are well written!

ff-6
From:	SMTP%"[email-masked]" 14-JAN-1994 08:54:35.07
Charles Letner

These are the paper on AMDER development, united and all-atom versions. 
Good for info on the actual parameterization.
1) Weiner & Kollman, J. Comp. Chem., Vol. 7, No. 2 230-252 (1986)
2) Weiner, et al., JACS, Vol 106, No. 3 (1984)

These are comparisons of some of the "bio" fields.
1) Hall & Pavitt, J. Comp. Chem., Vol. 5 No. 5, 441-450 (1984)
2) Whitlow & Teeter, JACS, 108, 7163-7172 (1986)
3) Kini & Evans, J. Biomol. Str. & Dyn., Vol. 9, No.3 475-488 (1991)
	also same authors and journal Vol 10, No. 2 265-279 (1992)

Next two are sort of interesting.  The first on comes down on AMBER and
CHARMM force fields; says that they may lead to totally false results. 
The second one is a response.  Note the authors here. ;)
1) Roterman, Gibson, & Scheraga,  J. Biomol. Struct. & Dyn, Vol. 7, No. 3
391-453 (1989).  Actually two paper in a series
2) Kollman & Dill, J. Biomol. Struct. & Dyn., Vol 8., No. 5, 1103-1107 (1991)

ff-7
From:	SMTP%"[email-masked]" 11-JAN-1994 18:05:50.78
Jeff Nauss

I am interested in whatever references you may come up with.  In the
meantime, here are some that might help with the CVFF forcefield used
by Biosym:

Maple et al. PNAS 85, 5350 (1988)
Hagler et al. JACS 101, 5131 (1979)
Hagler et al. JACS 101, 5122 (1979)
Lifson et al. JACS 101, 5111 (1979)

Then there is:

Stouch et al. J. Comp Chem 12, 1033 (1991)
Williams & Stouch, J. Comp Chem 14, 1066 (1993)

ff-8
From:	SMTP%"[email-masked]" 12-JAN-1994 01:16:53.72
Tracy Nero

Here are a couple of refs for you. I hope they help. If I come across
more (which I know I have at home) I'll mail them to you.

COMFA see J. Med. Chem.,1993, vol 36, 70-80
Tripos force field see J. Comp. Chem.,1989, vol 10, 982-1012
Molecular Mechanics , ACS Monograph, 1982, page 177 U. Burkert and N.L.Allinger
AMBER force field see J. Am. Chem. Soc., 1984, vol 106, 765-
                      J. Comp. Chem., 1986, vol 7, 230-

ff-9
From:	SMTP%"[email-masked]" 12-JAN-1994 08:33:43.53
gus mercier

In the QCPE bulletin v. 12 no. 1 1992 p.6-11 there is an extensive
bibliography of MM2 parameters.

[email-masked]

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