I think that opinion has changed over time and now most people
would recommend use of GB solvation instead of a distance dependent
dielectric. this avoids (at least mostly) both of the points you raise
below.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
烨 武 wrote:
> I'm sorry to ask questions again which may be asked frequently.
> I have read some letters about this items in the archive, but I am
> still confused about these questions, so please help!
> I want to minimize a structure of a protein considering the solvent
> effects but excluding explicit water.
> In the Frequently Asked Questions
> (FAQ)("http://amber.ch.ic.ac.uk/Questions/dielc.html), it said:
> "In the case of excluding explicit water the distance dielectric model
> seems to be the most fashionable,------"
> But I still have two question:
> 1.In this situation, when we use the distance dielectric model, which
> value should we choose for dielectric constant, 1 or larger,in order
> to model the water surrounding better?
> 2. In above distance dependent dielectric setting, will the software
> use the same dielectric constant value when computing the
> electrostatic interactions between two atoms separated by other
> protein atoms and two atoms seperated by surrounding waters (if the
> distance is the same)?
> If it is true, I think it is unreasonable, itn't it?
> Thank you for your help!
> Zheng Canhui
>
>
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Received on Mon Apr 11 2005 - 14:53:01 PDT
