[gmx-users] What algorithm does g_sas use?

[Matthew Zwier]

Hi Guang,

Be careful with this tool. It's very fast and very good at what it's
designed to do, but it does not appear to be designed to give accurate
single-residue SASA (as you will read in the paper on the method employed).
Definitely use g_sas for entire proteins or large cavities (it's blazing
fast), but consider MSMS or DSSP for single-residue data.

Matt Zwier


On Wed, Nov 7, 2012 at 1:26 AM, jia jia <jzg579 at gmail.com> wrote:

> Thanks!  I've checked  gromacs v 4.5.5 and got it.
> Seems all version before 4.0.5 doen't have that information..
>
> Cheers
> Guang
>
>
> 2012/11/7, Justin Lemkul <jalemkul at vt.edu>:
> >
> >
> > On 11/7/12 1:18 AM, jia jia wrote:
> >> Dear gmx users:
> >>     So sorry for bother you. Does any one know what algorithm g_sas
> >> use? There is no information about algorithm in help file, man page,
> >> and code. I think gromos use naccess method but not sure  gromacs  use
> >> the same one.
> >>
> >
> > References are printed in the screen output when running g_sas.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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