On Thu, Oct 24, 2013 at 10:35 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> 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
sulfur).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 24 2013 - 08:00:04 PDT
