AMBER: Antechamber Charge Calculation Method

From: A Box <boxtwin2.gmail.com>
Date: Tue, 30 Jan 2007 11:46:42 +1100

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 31 2007 - 06:07:28 PST
Custom Search