[gmx-users] Cavity detection on membrane protein surface

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 22 14:40:01 CET 2011

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 
may help.

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