Re: [AMBER] ATP and Mg2+ parameters

From: Alessandro Contini <alessandro.contini.unimi.it>
Date: Tue, 08 Jul 2014 12:50:50 +0200

Hi Valentina,
check in the amber parameters database

http://www.pharmacy.manchester.ac.uk/bryce/amber/

Updated parameters for divalent ions are also present in the
AmberTools14 distribution, accordingly to JCTC 2013, 9, 2733-2748 and
JCTC 2014, 10, 289-297

Hope this help.

Best regards

Alessandro

Il 08/07/2014 12:41, Valentina Romano ha scritto:
> Dear Amber users
>
> I would like to run a MD for a protein kinase in complex with ATP and a Mg2+ ion.
>
> Do you know if parameters for ATP and Mg2+ already exist?
> Or should I use antechamber?
>
> Thank you.
>
> Best,
> valentina
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
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>


-- 
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
ResearcherID: F-5064-2012
URL: http://www.researcherid.com/rid/F-5064-2012
skype alessandrocontini
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Received on Tue Jul 08 2014 - 04:00:04 PDT
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