AMBER Archive (2005)

Subject: Re: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 08 2005 - 13:28:23 CST

On Tue, Feb 08, 2005, Fabien Cailliez wrote:
>
> I have a question about dielectric constant in MMGBSA calculation with
> AMBER8. When I tried to put intdiel=2, I had a message that said me thta
> intdiel must be equal to dielc. Thus I put dielc=2 too, but I am confused
> with the results I obtained.

It sounds like you have not applied bugfix 27; is that the case?

>
> PS : I went through the code and I understood that when dielc is set to
> 2, the charges are divided by sqrt(2),

This should not be the case, if you have applied the bugfix.

(Note that we are not yet recommending that MMGBSA be run with interior
dielectric other than unity. The value, if any, of using intdiel=2 is still
a research problem.)

....dac
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