Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB

From: Jason Swails <>
Date: Thu, 24 Oct 2013 10:52:44 -0400

On Thu, Oct 24, 2013 at 10:35 AM, Vlad Cojocaru <> wrote:

> Dear Jason,
> I am rather new to GB calculations. I just want to double check
> something with you. In the email below you mentioned that the born
> radius meant for CT in mbondi3 is 1.8.
> However, I did some checks using parmed (using changeRadii and
> printDetails commands) on my topology files and the CT is assigned a
> radius of 1.7 regardless of which radii set (mbondi, mbondi2, mbondi3).
> Was the "1.8" from your email a mistake or there is something wrong in
> the way parmed is changing the radii ?

1.8 is a mistake. The real value is 1.7 (I verified this in the tleap
source code). Sorry for the confusion (1.8 is the radius used for

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 24 2013 - 08:00:04 PDT
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