AMBER Archive (2006)

Subject: AMBER: partial charges

From: Fabian Alejandro Rodriguez (far217_at_nyu.edu)
Date: Tue Oct 10 2006 - 11:35:53 CDT

Hello,
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?

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.

Thank you,
fabian.

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