[gmx-users] Cavity detection on membrane protein surface

[Mark Abraham]

On 23/11/2011 12:33 AM, Alex Jemulin wrote:
> Dear all,
> I'm studying a membrane protein. During MD some concavities appear and 
> disappear on its surface.
> I'd like to isolate atoms and residues involved in these formations.
> Any suggestion? Which steps should I follow to automate the 
> identification process?
>

g_rms can fit based on the whole protein and measure the RMS deviation 
based on just a subset of the protein. So I suggest making a large 
number of groups that appeal to you and scripting g_rms to loop through 
them. 
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts 
may help.

Mark
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