AMBER Archive (2004)

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

From: Jose Ramon Blas (jramon_at_mmb.pcb.ub.es)
Date: Thu Jan 22 2004 - 15:38:03 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.

Hope this helps,

Blas

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona

On Thu, 22 Jan 2004, tang kwa wrote:

> Dear All,
>
> TO neutralize the system containing DNA and water,
> LEaP module can be used to add Na+ ions. Could anyone
> tell me how Na+ ions are placed, at positions of
> bisector O1P-P-O2P, or iterative electrostatic
> calculations?
> Many thanks inadvance.
>
> Yours,
> Tangkwa
>
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