Re: [AMBER] Calculating Amber Force fields from Wikipedia

From: Kevin Hauser <84hauser.gmail.com>
Date: Tue, 16 Mar 2010 20:41:08 -0400

Hi, Dan,


The essence of the AMBER force fields is not a particularly easy thing to
conceptualize. Perhaps a review of the (not wikipedia!) literature on this
issue could help(?):

1
A Second Generation Force Field for the Simulation of Proteins, Nucleic
Acids, and Organic Molecules
Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth
M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James
W. Caldwell, Peter A. Kollman
J. Am. Chem. Soc., 1995, 117 (19), pp 51795197
*DOI: *10.1021/ja00124a002
Publication Date: May 1995

2
Force Fields for Protein Simulation
Jay W. Ponder & David Case
Advances in Protein Chemistry, 2003

3
Comparison of multiple Amber force fields and development of improved
protein backbone parameters.

Hornak V<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hornak%20V%22%5BAuthor%5D>,
Abel R <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Abel%20R%22%5BAuthor%5D>,
Okur A <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Okur%20A%22%5BAuthor%5D>,
Strockbine B<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Strockbine%20B%22%5BAuthor%5D>,
Roitberg A<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Roitberg%20A%22%5BAuthor%5D>,
Simmerling C<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Simmerling%20C%22%5BAuthor%5D>
.
Proteins. <javascript:AL_get(this,%20'jour',%20'Proteins.');> 2006 Nov
15;65(3):712-25.

4
Refinement of the AMBER Force Field for Nucleic Acids: Improving the
Description of a/g Conformer,
<http://simmerlinglab.org/wiki/index.php/Image:ParmBSC0.2007.pdf>
Biophys. Journ., 2007, Modesto
Orozco<http://simmerlinglab.org/wiki/index.php/Image:ParmBSC0.2007.pdf>

5
Andrew Leach, Molecular Modeling: Principles and Applications (Textbook)


Hope this helps...


On Tue, Mar 16, 2010 at 7:09 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> this is missing the point. It's not that the equation is wrong, its that
> it's more complex than the equation indicates, or can be made to simply
> indicate. There is 1-4 scaling, and excluded atom lists, and multiple
> phases
> for dihedrals, and skipping duplication of 1-4s in rings, and so on. The
> equation gives the basics, but the actual calculation involves significant
> logic checking and checking various arrays that are built based on
> knowledge
> of the topology of the system, not just coordinates. The equation as listed
> doesn't even work for methane. There is no simple way to "correct" it,
> though; one needs to understand the logic behind the force field, not just
> the parameters.
>
> On Tue, Mar 16, 2010 at 5:30 PM, Whimsica.aol.com <whimsica.aol.com>
> wrote:
>
> > I would be much more comfortable with a corrected Amber equation if one
> > exists that is good enough for simulating just nucleic acids for k12
> > students.
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
(631) 913.3194
(561) 635.1848
84hauser.gmail.com
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Received on Tue Mar 16 2010 - 18:00:04 PDT
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