[gmx-users] g_sas

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 15 17:34:38 CET 2012

afsaneh maleki wrote:
> Hello dear user,
> I have a system that is contained protein-water-ions. I used the
> following command:
> g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
> atom_area –q -nopbc
> I select the whole protein first for calculation, and then this protein
> for output.In this way I can obtain Area per residue from "res_area" file and
> area per atom from "atom_area" file.
> How to get area per residue with data of area per atom from "atom_area"
> file? When I average on area per atoms for a selected residue, it
> doesn't correspond with area per residue for a selected residue from
> "res_area".

It shouldn't.  Averaging the areas per atom should not produce anything related 
to the constituent residue(s).  The sum of the atom areas should yield the 
residue area.  A quick look through the code seems to indicate that this is 
true, that is, the two quantities are not produced independently; residue area 
arises from atom area.


> How to correlate area per residue for a selected residue with area per
> atoms for a selected residue?
> Thanks in advance,
> Afsaneh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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