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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Received on Mon Apr 18 2005 - 09:53:01 PDT
