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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Received on Wed Oct 11 2006 - 06:07:21 PDT
