AMBER Archive (2009)

Subject: Re: [AMBER] polarizable force field for 18-crown-6

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Fri Apr 17 2009 - 02:48:03 CDT

As far as I know, nobody developed polarizable parameters, including
"polarizable" charges for 18-crown-6. But it could be done.
For example charges could be obtained in interative way for fragments from
which the whole crown could be combined.

I would not mixed polarizable peptide with non-polarizable.

Piotr

On Thu, 16 Apr 2009, Gert von Helden wrote:

> From: Gert von Helden <helden_at_fhi-berlin.mpg.de>
> Sender: amber-bounces_at_ambermd.org
> To: amber_at_ambermd.org
> Date: Thu, 16 Apr 2009 19:33:15 +0200
> Subject: [AMBER] polarizable force field for 18-crown-6
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
>
> Hi,
> I am running some calculations on a gas-phase peptide - 18-crown-6 complex.
> I generate structures via REMD and then optimize selected structures via DFT
> (BP86). Using the ff99SB force field, the peptide backbone does not seem to
> be right. There is a section which might (should) be beta-sheet like. When I
> run the REMD calculations and impose contraints to give be beta sheet
> structures, the final DFT structures are lower in energy, compared to those
> obtained from unconstrained REMD (which are nowhere close to beta sheet
> like).
> Might using a polarizable force field (such as amoeba or ff02) give me
> "better" results? If so, did anybody generate polarizable force field
> parameters for 18-crown-6? Is it involved to do so? Also, could one mix force
> fields to describe the peptidic part using a polarizable force field and the
> 18-crown-6 part using a standard force field?
>
> Thanks in advance,
> Gert
>
> -------------------------------------
> Gert von Helden, Ph.D.
> Fritz-Haber-Institut der Max-Planck-Gesellschaft
> Faradayweg 4-6
> 14195 Berlin
> Germany
> tel.: +49-30-8413 5615
> fax: +49-30-8413 5603
>
>
>
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