AMBER Archive (2005)

Subject: AMBER: Geometrical distortion because of charge?

From: peng79_at_email.unc.edu
Date: Mon Mar 14 2005 - 12:21:28 CST

Hi,

We have been running MD simulations with cisplatin (CP) bound to 12mer dsDNA.
Our first simulations using charges reported in the literatures. We have
obtained charges from Gaussian 03 calculation using 631Gd and
LanL2DZ(exclusively for Pt) basis functions. The Pt is supposed to be in a
square planar conformation. Our simulations using Amber 8 with published
charges maintain the Pt geometry. However when we use the charges from
Gaussian, the two free amines of CP move towards each other and the N-Pt-N
angle changes from 91 degree to 58 degree. The original Pt charge is 0.709
and the new charge from Gaussian is 0.9131. The original charge of amine N is
-0.648 and that of Gaussian is -1.3219, significantly more negative. We are
not sure why the geometry of Pt is not maintained with the Gaussian charges
using Amber8. Looking forward to suggestions. Thanks.

Peng
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