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
--
========================================
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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