AMBER Archive (2008)

Subject: Re: AMBER: Glycam

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Thu Nov 06 2008 - 09:01:48 CST

Glycam06 does not incorporate polarization. Glycam04EP models lone
pairs (as "extra points") which can theoretically be made to mimic
some aspects of polarization, but that isn't the point of the
parameter set. I'm guessing the paper you mention is work from Denny
Elking, et al.?

Someone else will have to answer about gaussian polarizability in
protein models.

:-) Lachele

On Wed, Nov 5, 2008 at 11:02 PM, Neha Gandhi <n.gandhiau_at_gmail.com> wrote:
> Hi there,
>
> I have a query. I read a paper on incorporating charge polarization in
> Glycam. I wanted to if the Gaussian polarization model is incorporated
> in Glycam06 version. I realised that most of the references point to
> AMBER development, where this model was incorporated in Amber in 2005.
> But is there any gaussian polarization model for proteins for example
> in ff02 or ff02 EP version?
>
> Thank you very much , Awaiting your responses,
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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