[gmx-users] g_sas : Total surface area

[Kavyashree M]

Sir,

Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.

Kavya


On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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