AMBER Archive (2008)

Subject: Re: AMBER: amber ff and how it deals with out-plane chiral C

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jul 22 2008 - 06:57:04 CDT

Hi Alan-
why should improper terms be needed for tetrahedral carbon?
as far as I know those were only used for united atoms models. in
all-atom models, the 3-body angles do a fine job at keep the carbon tetrahedral.
maybe it would help us if you specify what you mean by "amber ff",
since there are many variations, some all-atom and some united. whether
they have impropers or not may depend on which one you mean.
certainly the different force fields intendend to be used with Amber
have many differences (and similarities of course)

On Tue, Jul 22, 2008 at 3:59 AM, Alan <alanwilter_at_gmail.com> wrote:
> Hi List!
>
> I've read "here and there" that Amber FF doesn't use improper
> dihedrals parameters for tetrahedral carbon (out-of plane) and for
> that a set of torsionals would do the parametrisation.
>
> Disregarding some likely wrong assertions above, where would I find
> further information about this particularity in amber ff? I failed to
> find that in Amber manual 10.
>
> Many thanks in advance.
>
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
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-- 
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Carlos L. Simmerling, Ph.D.
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