Dear Amber Users,
I am using the MM-PBSA / GBSA method to calculate binding free energy of
ligands to DNA / RNA. I am getting a large negative values for the ELE term
of the MM energy. I find this puzzling because I have seen in the
literature, reports of a large positive value. What cut-off and dielectric
constant should I be using for a DNA duplex?
Thanks,
Seth
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Received on Wed May 14 2008 - 06:07:44 PDT
