AMBER Archive (2008)

Subject: Re: AMBER: Query related to implicit solvent EXTDIEL

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 06 2008 - 10:31:08 CST

On Wed, Feb 06, 2008, S.Sundar Raman wrote:

> I am willing to simulate 20mer peptide implicitly in lipid
> environment using GBSA method. I tried to simulate the peptide with EXTDIEL
> = 4. Unfortunately i could not find the EXDIEL value in my output file.

It is a deficiency (fixed in the next release) that the value of extdiel is
never printed. You can go to mdread.f and modify the code to print out its
value (look for the place where intdiel is printed, and add a "write"
statement).

You should know that using generalized Born with such a small exterior
dielectric has not been extensively tested, so you might want to be prepared
for odd results.

...thanks for the report...dac

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