On Mon, Apr 18, 2005, Nina Fischer wrote:
>
> 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?
The only thing that is consistent with the way charges are derived is to set
intdiel=1 (the default, and recommended value). You can, of course,
experiement with different values, but should treat that as a reasearch
project in itself.
....good luck...dac
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Received on Mon Apr 18 2005 - 16:53:00 PDT
