[gmx-users] g_sas

[afsaneh maleki]

Hi,

Thanks dear Justin for useful reply,

I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system first for calculation,
and then protein for output. The SAS_calculations of residue protein
are different in two ways.
I have two questions.

Q1- Why results are different in two ways?
Q2-Can anyone demonstrates clearly how residue SAS of protein
calculate in two ways?
Q3- what property or quantity do I can get from The SAS_calculations
of residue protein in two ways?

Best wishes,
Afsaneh


On 3/15/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>> 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
> MILES-IGERT Trainee
> 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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