[gmx-users] How to define protein surface residues

[Mark Abraham]

Lee Soin wrote:
> Thanks, but what I mean is to just find out the surface residues, not to 
> calculate the surface area.

So use g_sas to plot the area per residue and look at the ones for which 
it is non-zero.

Mark

> 2009/3/3 David van der Spoel <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>>
> 
>     Lee Soin wrote:
> 
>         Hello!
>         I'm trying to find the surface residues of a protein. Maybe this
>         should be calculated by myself and not using GROMACS. Can
>         anybody tell me a feasible procedure for doing so? Thanks!
> 
>     g_sas
> 
>         -- 
>         Sun Li
>         Department of Physics
>         Nanjing University, China
> 
> 
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> 
> 
>     -- 
>     David van der Spoel, Ph.D., Professor of Biology
>     Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>  
>     http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
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> 
> 
> 
> -- 
> Sun Li
> Department of Physics
> Nanjing University, China
> 
> 
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