From owner-chemistry@ccl.net Tue Sep 26 18:00:00 2006
From: "Lukasz Cwiklik cwiklik]~[gmail.com" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: polarisable force field for new molecule
Message-Id: <-32635-060926102400-6891-/qLyeICe3aDVF4dJzKtFMg*|*server.ccl.net>
X-Original-From: "Lukasz Cwiklik" <cwiklik]|[gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Tue, 26 Sep 2006 13:29:22 +0000
MIME-Version: 1.0


Sent to CCL by: "Lukasz Cwiklik" [cwiklik\a/gmail.com]
On 9/26/06, Bala Subramanian bala**igib.res.in <owner-chemistry|-|ccl.net> wrote:
> Sent to CCL by: "Bala  Subramanian" [bala|*|igib.res.in]
> Dear CCL users,
>
> I am working on nucleic acid-drug interaction. I am very new to this. I want to
>use polarisable force field to simulate the complex. I can use ff02 for my DNA
> in amber, but i dnt know how to generate polarisable ff for ligand or in general
> any new molecule.Someone please suggest me on how i can do this.
Hi,
Not so long ago I was preparing polarizable force field parameters for
simulations of small molecules in Amber. I found very useful the web
page of Ulf Ryde:
http://www.teokem.lu.se/~ulf/Methods/resp.html
I have also prepared a tutorial how to do such a parametrization step
by step. You can find it on my web page:
http://www.molecular.cz/~cwiklik/publ.html
(direct link: http://www.molecular.cz/~cwiklik/materials/resp_fitting.pdf)
Best regards,
Lukasz Cwiklik


-- 
Lukasz Cwiklik
http://www.molecular.cz/~cwiklik