AMBER Archive (2008)

Subject: AMBER: Free Energy Calculations - parameters for MM

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Tue May 13 2008 - 11:29:23 CDT

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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