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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