AMBER Archive (2006)

Subject: Re: AMBER: Hexahydrated Counterions

From: David A. Case (case_at_scripps.edu)
Date: Wed May 10 2006 - 10:32:31 CDT

On Wed, May 10, 2006, Mahalakshmi Sahasranaman wrote:
>
> I have constructed A-DNA (DNA duplex) using nucgen. I want to add
> hexahydrated Na+ counterions at a distance of 5 Angstrom to the phosphorous
> atom of the phosphate groups.
>
> "addions adna Na+ 0 " only adds Na+ ions. How to add hexahydrated Na+
> counterions at a distance of 5 angstrom to the phosphorous atom of the
> phosphate groups ?
>

I think you will probably have to construct this starting coordinates by hand,
(or by some other program) then read them into LEaP.

You should be sure that you really want to do this. Most people (including
me) would argue that a better alternative is either to use a fully hydrated
simulation, or to use generalized Born with Debye-Huckel theory for the
counterions.

...good luck...dac
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