[gmx-users] g_sas

[Cheong Wee Loong, Daniel]

Ah ok. Fair enough.  Thanks!



-----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 10:48 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] g_sas



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: 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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--
========================================

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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