[gmx-users] g_sas

[Chih-Ying Lin]

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.

=> 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?

=> 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 ??


=> How to calculate the surface area of a micelle ?

Thank you
Lin


















>> 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.
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