AMBER Archive (2005)

Subject: AMBER: dielectric constant

From: Nina Fischer (nfischer_at_informatik.uni-tuebingen.de)
Date: Mon Apr 18 2005 - 03:22:34 CDT

Dear Amber users,

I am using the GB/SA method (igb=2) in sander in order to calculate the
relative binding free energy of a protein-DNA complex in implicit solvent.

As i know, it is common to use a dielectric constant for the interior of
proteins in the range of 4 to 20.

Does someone know how I can decide which value I should choose?
Is there an "easy" way to determine the dielectric constant (intdiel) for
proteins and DNA?

Regards and thanks in advance,
Nina

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