[gmx-users] inquiry about SAS

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 3 16:51:34 CEST 2012

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


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