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
Complex Carbohydrate Research Center
220 Riverbend Road "One small step for Man,
Athens, GA 30602 one giant leap for Man-9"
Received on Mon Feb 10 2003 - 11:29:36 PST
