RE: AMBER: Antechamber Charge Calculation Method

From: Junmei Wang <>
Date: Mon, 29 Jan 2007 20:48:17 -0600

There is a tutorial on how to do this. Please go to to see details.
All the best

Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649

        -----Original Message-----
        From: []
On Behalf Of A Box
        Sent: Monday, January 29, 2007 6:47 PM
        Subject: AMBER: Antechamber Charge Calculation Method
        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 molecules.
        Andrew Box

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Received on Wed Jan 31 2007 - 06:07:30 PST
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