AMBER Archive (2006)

Subject: Re: AMBER: partial charges

From: David A. Case (
Date: Wed Oct 11 2006 - 11:17:48 CDT

On Tue, Oct 10, 2006, Fabian Alejandro Rodriguez wrote:

> I've got a basic question:
> How important are the partial charges for MD on a DNA duplex 11-mer when
> I've got 400 distance restraints on it?

Probably not all that important.

> My DNA is a DNA adduct with only one dG base modified with BPDE. The
> partial charges for different initial configuration of the BPDE-dG base
> (different orientation of the pyrene residue, i.e. intercalated, minor
> groove, etc) were calculated using antechamber (total charge -1) and
> then this modified base was incorporated into the duplex 11-mer in leap.

This sounds like a pretty reasonable procedure to me. Of course, the way to
check the sensitivity of the outputs to changes in the inputs is to actually
try changing things, and see what happens.


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