AMBER Archive (2006)

Subject: Re: AMBER: saltcon variable

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 24 2006 - 14:38:53 CDT

On Thu, Jul 20, 2006, Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:
>
> I am using Amber 9 to simulate a big dimeric protein which is highly charged
> (-41 in total). Bacause of the dimension of the system I am trying the
> implicit solven model GBSA. I found that the default salt concentration
> (saltcon) for Debye-Hukel screening is 0. I wonder if some salt effect
> modeling could be useful in treating such a charged system and if it could
> help to better simulate a water environment . If yes, what could be a
> reasonable salt concentration to use in the simulation? I found in some
> works on DNA that a 0.1 M value was used.

So-called "physiological" salt concentration is about 150 mM. Many in-vitro
experiments use a higher salt, however. You should think about what
conditions you really want to simulate.

...good luck...dac

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