[gmx-users] g_sas : Total surface area

[Kavyashree M]

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of "Total" sas
(legend S2 of area.xvg file) of the protein and "Total" sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Thank you
Kavya



On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> 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
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