about ion-amino group non-bonded distance

From: thenmalar rathinavelan <thenmalrr_at_yahoo.co.in>
Date: Sat 8 Dec 2001 05:30:00 +0000 (GMT)

Dear ambers!
            I have a doubt regarding the results that I have
got from the dynamics of my DNA triplex. I found that
during the dynamics one of the counter ion (Na+) is
strongly coordinated to O6 of the guanine, a water
molecule and also to O4 of the next thymine through
out the dynamics. But, at the same time the ion also
comes closer to the amino group of cytosine,
(base-paried with the guanine) most of the times. That
is the distance between the Nitrogen atom and the ion
is around 3A. Some times it falls around 2.5A also. I
like to know whether the force field is taking care of
the amino group-ion interaction or some thing is wrong
in my dynamics.

Note: The charge on the Na+ ion is not changed and no
restraints are imposed on the ion.

Anyone please tell your suggestion about this.

Thankyou very much in advance

Yours sincerely,

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Received on Fri Dec 07 2001 - 21:30:00 PST
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