Atomic Radii for GB Implicit Solvent

From: Aron Broom (broomsday_at_gmail.com)
Date: Fri May 11 2012 - 14:40:12 CDT

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I've been doing a bit of implicit solvent stuff with NAMD recently, but
I've been using AMBER parameter files. In AMBER for implicit solvent the
intrinsic radii are controlled through the parameter file, and are set when
making the parameter file in LeAP. In NAMD it seems like these values are
preset and one can adjust them with the intrinsicRadiusOffset parameter,
and so the radii set in my AMBER parameter file would be ignored, is this
true?

Thanks,

~Aron

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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