Re: [gmx-users] g_sas : Total surface area

[Kavyashree M]

I meant subset :)

On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M  wrote:

> Sir,
>
> Oh! I was using sunset index numbers for both. I am sorry. I will try
> that and see. First option as protein and next the subset. Thank you
> very much.
>
> Kavya
>
>
>
> On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 12/12/12 9:37 AM, Kavyashree M wrote:
>>
>>> Thank you very much for your replies.
>>>
>>> The system consists of a homodimer in tip4p dodecahedron box
>>> simulated using OPLSAA ff.
>>>
>>> The A B C here are the amino acids:
>>> A- S T N Q G P H
>>> B- A V L I M C F Y W
>>> C- D E K R
>>>
>>> So these are set in an index file and i used each one of these
>>> to calculate sasa in g_sas.
>>> When the g_sas calculation starts it specifies the number of
>>> hydrophobic atoms, one of the example -
>>> For the whole protein -
>>> 4644 out of 7590 atoms were classified as hydrophobic
>>> For group A of same protein -
>>> 702 out of 1424 atoms were classified as hydrophobic
>>> For group B of same protein -
>>> 2614 out of 3496 atoms were classified as hydrophobic
>>> For group C of same protein -
>>> 1328 out of 2670 atoms were classified as hydrophobic
>>>
>>> In this the number of hydrophobic atoms of A, B and C adds
>>> up to the total hydrophobic atoms in whole protein.
>>>
>>> but after the calculation is over the average values of "Total" sas
>>> (legend S2 of area.xvg file) of the protein and "Total" sas of A, B
>>> and C are given below
>>> Whole protein - 254.04nm^(-2)
>>> A - 175.87nm^(-2)
>>> B - 211.33nm^(-2)
>>> C - 264.65nm^(-2)
>>>
>>> I expected that the average total sas of Whole protein atleast
>>> approximately
>>> equal the sum of Total sas of A, B and C. If not why? All calculations
>>> are
>>> done for the same trajectory after equilibrating.
>>>
>>>
>> Are you selecting the correct groups when running g_sas?  For instance,
>> you should be selecting "Protein" for the surface calculation, and then
>> your custom subsets for output.  If you use the subsets for both surface
>> calculation and output, you will get an artificially inflated value that
>> includes extra surface area that is actually buried in the context of the
>> whole structure.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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 listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
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>>
>
>
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Re: [gmx-users] g_sas : Total surface area

[Kavyashree M]

Sir,

Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.

Kavya


On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul  wrote:

>
>
> On 12/12/12 9:37 AM, Kavyashree M wrote:
>
>> Thank you very much for your replies.
>>
>> The system consists of a homodimer in tip4p dodecahedron box
>> simulated using OPLSAA ff.
>>
>> The A B C here are the amino acids:
>> A- S T N Q G P H
>> B- A V L I M C F Y W
>> C- D E K R
>>
>> So these are set in an index file and i used each one of these
>> to calculate sasa in g_sas.
>> When the g_sas calculation starts it specifies the number of
>> hydrophobic atoms, one of the example -
>> For the whole protein -
>> 4644 out of 7590 atoms were classified as hydrophobic
>> For group A of same protein -
>> 702 out of 1424 atoms were classified as hydrophobic
>> For group B of same protein -
>> 2614 out of 3496 atoms were classified as hydrophobic
>> For group C of same protein -
>> 1328 out of 2670 atoms were classified as hydrophobic
>>
>> In this the number of hydrophobic atoms of A, B and C adds
>> up to the total hydrophobic atoms in whole protein.
>>
>> but after the calculation is over the average values of "Total" sas
>> (legend S2 of area.xvg file) of the protein and "Total" sas of A, B
>> and C are given below
>> Whole protein - 254.04nm^(-2)
>> A - 175.87nm^(-2)
>> B - 211.33nm^(-2)
>> C - 264.65nm^(-2)
>>
>> I expected that the average total sas of Whole protein atleast
>> approximately
>> equal the sum of Total sas of A, B and C. If not why? All calculations are
>> done for the same trajectory after equilibrating.
>>
>>
> Are you selecting the correct groups when running g_sas?  For instance,
> you should be selecting "Protein" for the surface calculation, and then
> your custom subsets for output.  If you use the subsets for both surface
> calculation and output, you will get an artificially inflated value that
> includes extra surface area that is actually buried in the context of the
> whole structure.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] g_sas : Total surface area

[Justin Lemkul]

On 12/12/12 9:37 AM, Kavyashree M wrote:

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of "Total" sas
(legend S2 of area.xvg file) of the protein and "Total" sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.



Are you selecting the correct groups when running g_sas?  For instance, you 
should be selecting "Protein" for the surface calculation, and then your custom 
subsets for output.  If you use the subsets for both surface calculation and 
output, you will get an artificially inflated value that includes extra surface 
area that is actually buried in the context of the whole structure.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] g_sas : Total surface area

[Kavyashree M]

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of "Total" sas
(legend S2 of area.xvg file) of the protein and "Total" sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Thank you
Kavya



On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri
wrote:

> Hi Kavya,
> Can you better describe your system?
> As Mark suggested, could you supply some number?
>
> Francesco
>
>
> 2012/12/12 Mark Abraham 
>
> > On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M  wrote:
> >
> > > Dear users,
> > >
> > > I was calculating solvent accessible surface area for a trajectory
> > > using g_sas. I used an index file with 3 sets (A, B, C) of mutually
> > > exclusive residues but summing up to 20 amino acids. Then using
> > > g_sas calculated sas for these 3 sets separately and whole protein
> > > separately for the same trajectory.
> > > I was expecting that the average value of
> > > Total surface area (protein) ~ Total surface area (A)+Total surface
> area
> > > (B)+Total surface area (C)
> > > But it is not so.
> > > Could anyone explain me why?
> > >
> >
> > Not without seeing any numbers. You're probably thinking that the surface
> > area of A excludes the interfacial area to the other sets, but it
> doesn't.
> >
> > Mark
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
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> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] g_sas : Total surface area

[francesco oteri]

Hi Kavya,
Can you better describe your system?
As Mark suggested, could you supply some number?

Francesco


2012/12/12 Mark Abraham 

> On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M  wrote:
>
> > Dear users,
> >
> > I was calculating solvent accessible surface area for a trajectory
> > using g_sas. I used an index file with 3 sets (A, B, C) of mutually
> > exclusive residues but summing up to 20 amino acids. Then using
> > g_sas calculated sas for these 3 sets separately and whole protein
> > separately for the same trajectory.
> > I was expecting that the average value of
> > Total surface area (protein) ~ Total surface area (A)+Total surface area
> > (B)+Total surface area (C)
> > But it is not so.
> > Could anyone explain me why?
> >
>
> Not without seeing any numbers. You're probably thinking that the surface
> area of A excludes the interfacial area to the other sets, but it doesn't.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] g_sas : Total surface area

[Mark Abraham]

On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M  wrote:

> Dear users,
>
> I was calculating solvent accessible surface area for a trajectory
> using g_sas. I used an index file with 3 sets (A, B, C) of mutually
> exclusive residues but summing up to 20 amino acids. Then using
> g_sas calculated sas for these 3 sets separately and whole protein
> separately for the same trajectory.
> I was expecting that the average value of
> Total surface area (protein) ~ Total surface area (A)+Total surface area
> (B)+Total surface area (C)
> But it is not so.
> Could anyone explain me why?
>

Not without seeing any numbers. You're probably thinking that the surface
area of A excludes the interfacial area to the other sets, but it doesn't.

Mark
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