AMBER Archive (2007)

Subject: Re: AMBER: calcium and zinc parameter

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Thu Dec 06 2007 - 07:21:10 CST

I don't think but, anyway, you create them.
I'm sorry but I'm not so useful for this kind of information.
Regards

mattia


Taufik Al-Sarraj ha scritto:

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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**-**-**-**-**-**-**-**-**-**-**-**-**
 
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
----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu