GB and Ions, 2nd try

From: Andreas Svrcek-Seiler <>
Date: Tue 2 Oct 2001 17:43:39 +0200 (CEST)

Dear experts,
According to literature,
rborn for Magnesium = 1.35 A (Journ. Chem. Phys. 111,21,1999).
However, if a Mg2+ ion is added to a RNA molecule,
(using LEaP) and the systems is subsequently minimized with GB,
the ion moves away from the RNA, following the gradient.
A closer look shows that E_Coul + E_GB is repulsive up to a
distance (centroid RNA -> Ion) of (very) roughly 12 A and then slowly
rising as one would expect from a damped Coulomb potential.
Only by increasing rborn to ~2.0-2.8 A, the NA-Ion interaction becomes
(strongly) attractive for short distances.
Now: Is arbitrarily increasing rborn a stupidity or physically justified
( or justified according to the principle 'if it works, it's ok') ?
Or are Ions simply beyond the scope of the model ?

Thanks in advance for any answers
Best regards
W. A. Svrcek-Seiler

P.S.: I expect the same behavior for monovalent cations,
      but I haven't tried yet.

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Received on Tue Oct 02 2001 - 08:43:39 PDT
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