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

From: Romain M. Wolf <>
Date: Mon, 21 Nov 2016 10:01:31 +0100

Using gbsa=2 in sander (no gradients with this setting, used for single coordinate sets only), results seem very close to those obtained with molsurf (at least in some examples I have tried for evaluating the SASA in MMGB/SA computations). The LPCO method usually generates somewhat smaller contributions of SASA.
With molsurf itself, I have sometimes experienced problems in my MMGB/SA protocols. For a small fraction (1% of less) of instantaneous frames, molsurf (called from NAB) fails (for reasons I have not been able to figure out).


Romain M. Wolf

> On 18 Nov 2016, at 21:15, David A Case <> wrote:
> 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 (
> ...dac
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Received on Mon Nov 21 2016 - 01:30:04 PST
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