[gmx-users] g_sas

[Cheong Wee Loong, Daniel]

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?



-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] 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: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at 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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--
========================================

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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