[gmx-users] Cavity detection on membrane protein surface
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users