[gmx-users] g_sas

Fri Apr 24 07:47:07 CEST 2009

Hi all.  Thanks for all your replies.  I think I understand it now and can definitely see how having the calculation and output group would add to the flexibility and utilty of g_sas.

Thanks.

Daniel

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Friday, April 24, 2009 1:30 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas

Hi,

Of course you can. But if part of Protein A is buried in an interface,
doing the SAS calculation over A only will also include the surface
interface; it will give the total surface of A. That may actually be
handy if you want to determine what the buried surface is. You
calculate the total surface for protein A and the total surface for
A+B. In both cases you use Protein A for the output. Then subtracting
one from the other gives the buried surface area. So it makes sense
calculating the area over Protein A, but it's just something
different.

Hope it's clear.

Cheers,

Tsjerk

On Fri, Apr 24, 2009 at 4:48 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>> you.
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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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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