AMBER Archive (2007)

Subject: Re: AMBER: calcium and zinc parameter

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Dec 05 2007 - 12:43:45 CST

Hi Mattia,
Thank you for the link below. I have a question. Do you know if i can
study DNA strand(s) on Si or Au surfaces, are there forcefields that
describe theses surfaces in AMBER.

Thank you for your help,
Taufik

Mattia Mori - CERM wrote:
> In this paper you can find good Zinc parameters for Amber Force Field
>
> Tuccinardi T, Martinelli A, Nuti E, Carelli P, Balzano F, Uccello-Barretta
> G, Murphy G, Rossello A.
> /Bioorg. Med. Chem/. 2006 14(12),
> 4260-4276
>
> Or you can download
>
> http://www.mmvsl.farm.unipi.it/downloads/free-downloads/amber-ff-parameters-for-the-zinc-hydroxammate-interaction/
>
>
> For Calcium ions you can find parameters in related papers or databases.
>
> Regards
>
> Mattia
>
>
>
>
>
>
>
>
> Madjid Taghdir ha scritto:
>> Dear amber users,
>> Hi
>> I am trying to simulate a protein with two heteroatom (Ca and Zn) that
>> cordinated to its structure. how can I find the force constants and
>> equilibrum bond , angle and so on.
>>
>> Best regards
>>
>> Tghdir
>>
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> --
>
>
>
>
>
>
> **-**-**-**-**-**-**-**-**-**-**-**-**
>
> Mattia Mori, PhD Student
> CERM - Centro di Risonanze Magnetiche
> via L. Sacconi 6,,
> 50019 Sesto Fiorentino, FI
> fax (+39) 055 4573914
> tel (+39) 055 4573912
> www.cerm.unifi.it
>
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