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<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I would like to calculate
the RMS fluctuations of residues in an active site, using the following command
and options:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>g_rmsf -f x16traj.trj -s
x16topol.tpr -n index2.ndx -b 1000 -res -o rmsf.xvg -od rmsdev.xvg<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>When the program asks me to
"Select group(s) for root mean square calculation", <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I select the appropriate
group number. This gives me rmsf.xvg and rmsdev.xvg files which only contain
values for the residues specified in the group I selected. I am focusing on
rmsf.xvg, as that has the RMS fluctuation data.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I have groups defined for
the entire active site, as well as several sub-regions of it. Several residues
occur in more than one sub-region.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I notice that the values I
get for RMSF for the same residue differ, depending on which group I have
chosen. (i.e. value for a given residue, when the whole pocket is selected as
the group, is different from when I only select a sub-pocket containing that
residue).<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Is g_rmsf somehow referring
the coordinates of this residue's atoms to a constantly-changing reference
frame? It seems to me that the residue's RMSF(as an average of the RMSF of its
atoms) should only be in reference to the average position of its atoms, and
not dependent upon some external "frame".<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Should I just use the whole
protein as the reference, and extract the residue values of interest by hand?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> Keith</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p style='margin-bottom:0in;margin-bottom:.0001pt'><font size=2
face="Times New Roman"><span style='font-size:10.0pt'>============================<br>
</span></font><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Keith D. Ball, PhD<br>
Staff Scientist<br>
Catalyst Biosciences<br>
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size=2><span style='font-size:10.0pt'><br>
<br>
</span></font><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>650-266-8661 (phone)<br>
650-871-2475 (fax)<br>
<a href="mailto:kball@catbio.com">kball@catbio.com</a></span></font><font
face=Verdana><span style='font-family:Verdana'><o:p></o:p></span></font></p>
<p style='margin:0in;margin-bottom:.0001pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'><a href="http://www.catbio.com">http://www.catbio.com</a></span></font><font
size=2><span style='font-size:10.0pt'><br>
============================<o:p></o:p></span></font></p>
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