Cheong Wee Loong, Daniel wrote:
Thanks for the explanation. It is much clearer now. Although I still don't
quite understand why we can't just use Protein A as the calculation group AND
output group to find the SASA of protein A. I know it states that the
calculation group should be all non-solvent atoms, but I guess I am just
trying to understand why. As in why do we need both the calculation and
output groups in the first place? Why can't we just use the group of atoms
that we are want to find the SASA for?
That information is probably contained in the references that g_sas asks you to
read and cite.
-Justin
-----Original Message----- From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent:
Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re:
[gmx-users] g_sas
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: [email protected]
[mailto:[email protected]] 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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This email is confidential and may be privileged. If you are not the
intended 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
========================================
_______________________________________________ gmx-users mailing list
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This email is confidential and may be privileged. If you are not the intended
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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