[gmx-users] g_sas

[David van der Spoel]

On 4/3/10 8:36 PM, Justin A. Lemkul wrote:
>
>
> Chih-Ying Lin wrote:
>>
>> 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, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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