Re: [AMBER] GDP and MG parameters

From: FyD <>
Date: Tue, 28 Aug 2012 12:15:54 +0200


You might look in R.E.DD.B.; See the F-90 & F-91 projects:

You will find many FF libraries for more than 200 cofactors; GMP, GDP,
GTP are obviously available...

regards, Francois

> I am looking into starting simulations of a protein that has a GDP and a
> MG ion in the active site.
> I know that in the database of AMBER parameters there are the Carlson
> parameters for GDP and the new Sorensen parameters for MG.
> I also found this comment from David Case which made me wonder about
> GDP. Is there anything new on the paper mentioned there ?
> I also read carefully this thread.
> Before starting simulations, I would be very grateful if people that
> have been using these parameter sets would comment on their experience
> with them (besides what is published in the respective references).
> If people are aware of other parameter sets, not available in the data
> base but worth trying out, I would also be very interested.
> Best wishes
> Vlad

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Received on Tue Aug 28 2012 - 03:30:07 PDT
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