Andrew,
There is a tutorial on how to do this. Please go to
http://amber.scripps.edu/antechamber/example.html to see details.
All the best
Junmei
==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang.encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu]
On Behalf Of A Box
Sent: Monday, January 29, 2007 6:47 PM
To: amber.scripps.edu
Subject: AMBER: Antechamber Charge Calculation Method
Hi
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
