[gmx-users] g_sas : Total surface area

[Kavyashree M]

I meant subset :)

On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> 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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>
>