AMBER Archive (2007)

Subject: Re: AMBER: calcium and zinc parameter

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Tue Dec 11 2007 - 07:07:31 CST

Dear Taghdir
Maybe you have a new protein...Generally you should run QM calculation with GAUSSIAN or GAMESS to compute the charge of your Calcium ions on the system.
Then you should build a library or a new force fields, it depend on the relevance of Calcium in your calculations.

Good luck

mattia

Madjid Taghdir ha scritto:

Dear Mattia
Hi
Thank you for your help and guidance.
However I could not find the Calcium parameters (yet).
 
Best regards
Taghdir 

----- Original Message ----
From: Mattia Mori - CERM <mori@cerm.unifi.it>
To: amber@scripps.edu
Sent: Wednesday, December 5, 2007 2:45:08 PM
Subject: Re: AMBER: calcium and zinc parameter

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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Questo messaggio è stato controllato dal Sistema Antivirus NOD32
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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