Subject: Re: CCL:Re: Parameterization

From: Rick Venable <[email-masked]>
Date: Fri, 18 Sep 1998 21:26:52 -0400 (EDT)

On Wed, 16 Sep 1998, Howard Alper wrote:
> Now I have some questions about parameterization to create forcefields
> for MD simulations.  Specifically, I am interested in parameterizing
> Nitromethane.  While any information regarding a set of parameters
> (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would
> be welcome, we are interested in generating the neccesary parameters,
> and in a form suitable for use in CHARMM.  To this end I have several
> questions: 

I've omitted the questions, because I'm not answering them directly, but
supplying some references from Alex MacKerell's web site at

	http://www.pharmacy.umab.edu/~alex/research.html

The papers below describe the development of various topology and
parameter sets which are distributed with the academic version of
CHARMM; additional citations and the parameter sets themselves (in
CHARMM format) are also available on the web page.  Typically, force
constants for bond stretching and angle bending are derived from
published IR/Raman spectroscopic data, after conversion to the CHARMM
system of units.  Atomic point charges and VDW radii parameters require
extensive ab initio calculations, while torsions are usually
parameterized to match experimentally determined rotational barriers
and/or conformational distributions.

MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; 
Evanseck, J.D.; Field, M.J.;  Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.;  Lau, F.T.K.; Mattos, C.; 
Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, W.E.;
Roux, B.;  Schlenkrich, M.; Smith, J.C.;  Stote, R.; Straub, J.;
Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom
empirical potential for molecular modeling and dynamics Studies of
proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.

Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
for the Optimization of Lennard-Jones Parameters. Journal of
Computational Chemistry, 1998, 19:  334-338. 

Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
Groups of Nucleotides. Journal of Computational Chemistry, (1997)
18:221-239. 

A.D. MacKerell Jr., J. Wi-rkiewicz-Kuczera and M. Karplus, An All-Atom
Empirical Energy Function for the Simulation of Nucleic Acids, Journal
of the American Chemical Society (1995)  117:11946-11975.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://www.erols.com/rvenable       \/   |=|    see   http://www.fda.gov  )

---

From: Per-Ola Norrby <[email-masked]>
Date: Mon, 21 Sep 1998 09:11:01 +0200

Howard Alper wrote:

 .....

>  Specifically, I am interested in parameterizing Nitromethane.
>While any information regarding a set of parameters (bond, angle,
>torsion, out-of-plane,charges,van der Waals, etc) would be welcome,
>we are interested in generating the neccesary parameters, and in a form
>suitable for use in CHARMM....

 .....

	Dear Howard,

	We just published a method for parameterization, specifically
implemented for MacroModel, but we put a lot of effort into making the
routines general enough so that you should be able to use it in a similar
manner with any MM program running under Unix.  Anything force field
specific is handled by Unix scripts, you only need to be able to handle
Unix to modify the method for the force field you are interested in.  The
method is described in J. Comput. Chem., 1998, 19, 1146-1166.  I'll share
the routines (note! they are NOT user-friendly, and you definitely need the
article to make sense of them).  Send me an email if you're interested.
The stuff I'm distributing right now is a year old, I'm right in the middle
of putting together an updated version, should be ready in a couple of
weeks.'

	Best regards,

	Per-Ola Norrby

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 *  Per-Ola Norrby, Associate Professor
 *  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], http://compchem.dfh.dk/