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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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