Re: [AMBER-Developers] About GB Atomic Radii for Calculating SASA

From: David A Case <>
Date: Fri, 18 Nov 2016 15:15:34 -0500

On Fri, Nov 18, 2016, Jason Swails wrote:

> I suspect more important than the radius set that you use will be the
> algorithm you use. For example, LCPO (the default used in sander) has the
> advantage of yielding analytical gradients for use in dynamics, but its
> theoretical underpinnings are more suspect than other algorithms, like the
> ones pbsa offers or what's available in molsurf.

Generally, one of the best ways to carry out SASA calculations is to use the
original Mike Connolly version of ms. This is packaged as a part of SHIFTS,
see my webite (


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Received on Fri Nov 18 2016 - 12:30:03 PST
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