AMBER Archive (2003)

Subject: Internal dielectric in MM-GBSA

From: Robert J. Woods (rwoods_at_ccrc.uga.edu)
Date: Mon Feb 10 2003 - 13:29:36 CST

Hi folks,

To more reasonably approximate the interior of a protein, we are interested
in using a value of the interior dielectric greater than 1, perhaps 3 or 4.
There are two variables that affect this in GB, namely, either by setting
dielc=n OR intdiel=n (done using a modified mm_pbsa.pl script)

Both give the expected results for <Eelec> that is, they scale it by 1/n.
But, they behave differently toward <GB>. Dielc=n scales <GB> by 1/n, but
intdiel scales by a little more. For example, (to keep the math clear) if I
set n=10 here is what I get:

dielc=1.0 (default) <Eelec> = 54.6, <GB> = -14.0

dielc=10.0 <Eelec> = 5.46, <GB> = -1.40

intdiel=10.0 <Eelec> = 5.46, <GB> = -1.25 <------

Shouldn't dielc and intdiel both scale <GB> by 1/n ?

Thanks,

Rob

Robert J. Woods, Ph.D.

Associate Professor of Biochemistry Voice: (706) 542-4454
 and Molecular Biology FAX: (706) 542-4412

University of Georgia http://glycam.ccrc.uga.edu
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