Cheong Wee Loong, Daniel wrote:
Thanks Justin for the reply. I did read the help and manual and understand
that the output file can be the whole or part of the calculation group. What
I don't quite understand is what the output group represents. I am assuming
that the calculation group would be the group of atoms that will be probed to
determine the solvent accessible are. If so, what does the output group
represent?
Consider the following situation. I have a protein complex of protein A and
protein B in explicit solvent with ions. The calculation group includes
everything that is non-solvent. Now let's say I only care about the SASA of
protein A. Therefore, protein A is my output group, and I get hydrophilic,
hydrophobic, and total SASA for protein A. I can similarly run the calculation
(with the same non-solvent calculation group) and output the SASA of protein B.
This is useful in that if the same calculation and output group is used, then
some of the detail of (in my example) the protein complex may be lost.
For an aqueous protein, this point is pretty moot, but the selectable output
group is a feature of most Gromacs tools to allow the user flexibility and
versatility.
-Justin
Thanks.
-----Original Message----- From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent:
Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas
Cheong Wee Loong, Daniel wrote:
Dear all,
I am interested to calculate the hydrophobic and hydrophilic area of the
surface of the protein layer I am simulating. It looked like g_sas would
be able to give me what I was looking for. But I was wondering what the
difference is between the calculation group and the output group. In
particular, what is the output group? I tried looking in the manual and in
the archives but I can't seem to find an answer to it.
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."
-Justin
Thanks.
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-- ========================================
Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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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recipient, please delete it and notify us immediately. Please do not copy or
use it for any purpose, or disclose its contents to any other person. Thank
you.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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