[gmx-users] g_sas

[David van der Spoel]

On 2010-04-05 02.35, Chih-Ying Lin wrote:
>
>
>
> Hi
>  From David,
> "If you select a
> group consisting of a single residue in a protein the SAS will be
> computed as if the rest of the protein is not there. Very useful when
> you want to compute protein-protein interface areas."
>
>
> => therefore, if i select a group consisting of a single residue, which
> is in the core of a protein, it is impossible that water penetrates into
> the core of the protein so SAS is supposed to be zero.
>
> => However, after calculation with g_sas, the SAS_calculation of the
> single residue residing in the core of the protein is NOT ZERO.

If you select the whole protein first for calculation, and then this 
single residue for output it should be very close to zero (if it is 
inside really). If you do what I described above you will get the total 
area of the residue as if the remainder of the protein wasn't there.

>
> => My understanding is that g_sas returns the surface area of the single
> residue and it does not matter where the single residue locates.
>       right?
>
> => The single residue can locate in the core of the protein or on the
> surface of the protein. The g_sas calculation for the single residue
> will not make a huge difference unless the single residue deforms/
> twists .....  on the surface or in the core of the protein,right ?
>
>
> => How to compute protein-protein interface area?
If you have protein A and B in complex you do three g_sas:

AB AB
A A
B B

the interface is now A + B - AB

>
> => In the protein + ligands + water system, I want to compute
> protein-ligand interface, protein-water interface, and ligand-water
> interface separately.  => How?
>
>
> => in the protein + water system, g_sas computes the total SAS
> fluctuating between   88  and  144  (angstrom_squares)
> => does it make sense ?
> => I don't think that protein will swell 50 % plus in the pure water.
> => But why ??
Look at the movie.
>
>
> => How to calculate the surface area of a micelle ?
>
> Thank you
> Lin
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>> > Hi
>> > The command
>> > g_sas => Select a group for calculation of surface and a group for output
>> >
>> >
>> > What is the difference between "a group for calculation of surface"
>> > and "a group for output"?
>>
>>  Please consult the documentation. From g_sas -h:
>>
>>  "The program will ask for a group for the surface calculation and a
>>  group for the output. 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."
>>
> Actually this documentation is not correct.
>
> The calculation group are those atoms taken into account in the
> computation, whether or not they are solvent accessible. If you select a
> group consisting of a single residue in a protein the SAS will be
> computed as if the rest of the protein is not there. Very useful when
> you want to compute protein-protein interface areas.
>
>>  -Justin
>>
>> > Thank you
>> > Lin
>> >
>>
>
>
> --
> David.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se