Subject: Re: CCL:Counter-ions on AMBER calculations

From: Eberhard von Kitzing <[email-masked]>
Date: Mon, 29 Jun 1998 14:00:52 +0200

Dear Andre Mauricio de Oliveira,

At 17:36 Uhr -0300 25.06.1998, andre mauricio de oliveira wrote:
>Can anyone tell me about simulation of counter-ions upon oligonucleotide
>backbones, employing any model such as Condensation Theory to avoid the
>use of explicit sodium, potassium or magnesium atoms  in AMBER force field
>calculations?

To calculate the transtion point between B-DNA and Z-DNA as a
function of ion concentration and ion size we used MSA theory.

>I'm interessed in setting any correction on the distance-dependent
>dieletric constant present in the coulombic term of AMBER forcefield wich
>includes charged atoms in the enviroment.

See:

Reinhard Klement, Dikeos Mario Soumpasis, Eberhard v. Kitzing and
Thomas M. Jovin (1990). "Inclusion of ionic interactions in force
field calculations of charged biomolecules - DNA structural
transitions." Biopolymers 29 1089-1103.

======================================================================

Eberhard von Kitzing

Max-Planck-Institut fuer Medizinische Forschung
Jahnstr. 29
D 69115 Heidelberg
Germanny

email: [email-masked]
WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/