[gmx-users] g_sas : Total surface area

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 15:46:10 CET 2012

On 12/12/12 9:37 AM, Kavyashree M wrote:
> 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.

Are you selecting the correct groups when running g_sas?  For instance, you 
should be selecting "Protein" for the surface calculation, and then your custom 
subsets for output.  If you use the subsets for both surface calculation and 
output, you will get an artificially inflated value that includes extra surface 
area that is actually buried in the context of the whole structure.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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