[gmx-users] g_sas

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 16 12:38:07 CET 2012

afsaneh maleki wrote:
> 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?

You're asking g_sas to do two different things.  You should note that g_sas 
tells you precisely how to do the calculation (from g_sas -h):

"The calculation group should always consists of all the non-solvent atoms in 
the system. The output group can be the whole or part of the calculation group."

Choosing the whole system for the calculation group is wrong and will give an 
answer that is likely not what is needed.

> Q2-Can anyone demonstrates clearly how residue SAS of protein
> calculate in two ways?

Refer to the literature cited in the g_sas screen output.  Those papers will 
contain the methods.  Your second method is, however, not appropriate.  The 
first method is.

> Q3- what property or quantity do I can get from The SAS_calculations
> of residue protein in two ways?

Likely a meaningful one and a useless one.



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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