[gmx-users] g_sas : Total surface area

Mark Abraham mark.j.abraham at gmail.com
Wed Dec 12 12:06:33 CET 2012

On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Dear users,
> I was calculating solvent accessible surface area for a trajectory
> using g_sas. I used an index file with 3 sets (A, B, C) of mutually
> exclusive residues but summing up to 20 amino acids. Then using
> g_sas calculated sas for these 3 sets separately and whole protein
> separately for the same trajectory.
> I was expecting that the average value of
> Total surface area (protein) ~ Total surface area (A)+Total surface area
> (B)+Total surface area (C)
> But it is not so.
> Could anyone explain me why?

Not without seeing any numbers. You're probably thinking that the surface
area of A excludes the interfacial area to the other sets, but it doesn't.


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