AMBER: Antechamber Charge Calculation Method

From: A Box <>
Date: Tue, 30 Jan 2007 11:46:42 +1100


I am trying to create a set of charges for a small molecule (around 140
atoms) with Antechamber. I can create the charge for the molecule (with the
required +1 charge), but my problem is that I need to connect this molecule
to a piece of DNA. When I delete a hydrogen from the molecule to connect it
the a DNA base pair, I end up with a molecule with a fractional charge. How
do I create a removable group for a molecule that has a net charge of zero
(for the atoms that are removed) and how do i calculate the charges for the

Andrew Box

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Received on Wed Jan 31 2007 - 06:07:28 PST
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