[gmx-users] g_sas

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 3 20:45:44 CEST 2010

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 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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