[gmx-users] sasa

[Frauke Meyer]

Hi David,

> On Thu, 2003-03-20 at 17:34, sadhna wrote:
> > HI,
> >     I would like to know which algorithm is implemented  in gromacs
> > for the calculation of SASA(ie g_sas)
> >
> If you run the program it will print the reference to the screen
> Eisenhaber 1995
> >

I still have some other questions concerning the SAS calculation:
1. The values for the SAS per atom in atomarea.xvg (unit: nm^2) are much
too high, it seems:
e.g.
                 surface in nm^2
  HE2 174 TYR 1684 0.384531  0.147864
  CZ  174 TYR 1685 0.812887  0.660785
  OH  174 TYR 1686 0.629811  0.396662
  HH  174 TYR 1687 0.723823  0.52392

with radii r(C)=0.16nm or r(H)=0.1nm
the maximal atom surfaces thenshould be
A(C)=r^2*pi*4=0.32nm^2 or A(H)=0.13nm^2. But the results are higher.

How can they be higher than the total area of the squere with this radius?
Is it maybe not the connolly surface but the center-sas, so the one of the
center of the probe sphere?

2. The last column is just the square of the SAS in the last but one
column. In the gmx-users list it was said it is the standard deviation.
but why is that just the square?

3. If the per atom surface is also just the SAS per atom, then the sum
over all atoms per residues should give the per residues SAS, right?
However, the sum of all per atom SAS is always slightly higher (5-10%)
than the
per residue SAS. Why is tht so?

Thanks,
all the best,
Frauke