[gmx-users] g_sas : Total surface area

[francesco oteri]

Hi Kavya,
Can you better describe your system?
As Mark suggested, could you supply some number?

Francesco


2012/12/12 Mark Abraham <mark.j.abraham at gmail.com>

> 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.
>
> Mark
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-- 
Cordiali saluti, Dr.Oteri Francesco