[gmx-users] sasa

[David van der Spoel]

On Thu, 2003-03-20 at 09:57, Frauke Meyer wrote:
> 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?
> 
You have to add the radius of the probe, for water usuall 0.14 nm, which
means that for H the max area would be 0.72, for C it would be  1.13
nm^2

> 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?
I don't know. Check the source...
> 
> 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?
Another good question with the same answer...
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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