Check Bryce group webpage
http://www.pharmacy.manchester.ac.uk/bryce/amber/
for all parameters. you can perform MD with Mg2+ and I think it is updated
in ions parameters in latest Amber version. You can just use load that to
set up parameters for Mg2+. You can treat ATP as separate ligand though and
run antechamber and make complex.
On Tue, Jul 8, 2014 at 12:41 PM, Valentina Romano <
valentina.romano.unibas.ch> wrote:
> 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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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue Jul 08 2014 - 04:00:03 PDT
