[gmx-users] inquiry about SAS

[Justin A. Lemkul]

On 7/3/12 10:49 AM, Turgay Cakmak wrote:
> Hi all,
>
> I am calculating SAS using g_sas of my system (several peptides in
> water and ions, Na and Cl). I choose:
>           for calculation group: non-water
>           for output group: protein
>   (400 out of 750 atoms were classified as hydrophobic)
>
> When I plot the Area vs time graphs, both the hydrophobic-SAS and
> hydrophilic-SAS decrease over the time. I think, the reason of the
> hydrophobic-SAS decrease from 65 nm2 to 30nm2 is due to aggregation of
> the peptides. But, I couldn't understant why hydrophilic-SAS is
> decreasing from 40 nm2 to 20nm2 over time. Do the results make sense?
>

Sure, you've got both hydrophobic and hydrophilic contacts happening.

> May be I mis-understand the meanings of the hydrophobic and
> hydrophilic SAS. Please, someone could explain it to me, I would be so
> glad.
>

These are merely subdivisions of total SASA.  Atoms are either polar 
(hydrophilic) or nonpolar (hydrophobic) and thus contribute to the total SASA 
based on their characteristics.

-Justin

-- 
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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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