On Thu, Oct 10, 2002, Pratul Agarwal wrote:
> A quick question -- what would be a good value of dielectric
> constant for the interior of proteins? I will really appreciate
> references for any published studies in this direction (AMBER
> and in general).
>
> Studies with other packages (e.g. GROMOS) report the use of
> values ranging from 17 to 20.
>
There is no "quick" answer-- it depends entirely on what you are planning
to do with the results, and how much explicit averaging of protein
conformations you are including. Remember that a dielectric constant
is a model for electrostatic relaxation. If you include this explicitly,
you don't need a dielectric model.
What I think is best:
a. for explicit solvent MD simulations, eps=1 everywhere.
b. for mm/pbsa or mm/gbsa with good sampling of the solute configurations,
use eps=1 for the solute, eps=80 for the water (plus use the saltcon
variable or equivalent for non-zero salt concentrations.)
c. for a single conformation of a protein, you can find recommendations
from 4 to 20 or so. There is lots of good evidence that there is no
"right" answer.
The literature on this subject is quite extensive, and you might as well go
ahead and read some of it.
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Oct 10 2002 - 11:33:19 PDT
