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On 23/11/2011 12:33 AM, Alex Jemulin wrote:
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cite="mid:1321968839.20502.YahooMailNeo@web132409.mail.ird.yahoo.com"
type="cite">
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<div style="RIGHT: auto">Dear all,</div>
<div style="RIGHT: auto">I'm studying a membrane protein. During
MD some concavities appear and disappear on its surface.</div>
<div style="RIGHT: auto">I'd like to isolate atoms and residues
involved in these formations.</div>
<div style="RIGHT: auto">Any suggestion? Which steps should I
follow to automate the identification process?</div>
<div style="RIGHT: auto"> <br>
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<br>
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. <a
href="http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts">http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts</a>
may help.<br>
<br>
Mark<br>
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