AMBER Archive (2004)

Subject: Re: AMBER: How does LEaP place Na+ ions?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jan 22 2004 - 11:17:32 CST

> As seems from the manual, a Coulombic potential is computed on the points
> of a grid (with a default grid-spacing of 1 angstrom). The ions are then
> placed in the best positions following this potential (for DNA them use
> to be placed near P groups).
>
> In this case, the electrostatic potential is not recomputed after each ion
> addition. Alternative procedures, that consider recomputation of potential
> after each ion is placed, have been published elsewhere, (see
> Proteins,(2001), 45, 428-4379), although for DNA this issue will not
> be critical.

The electrostatic potential is recomputed after adding each
ion, unless someone has rewritten the code.

Bill Ross

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