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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ming & Wall (2005) Quantifying
Allosteric effects in Proteins. PROTEINS: Structure, function and
bioinformatics<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><a
href="http://www3.interscience.wiley.com/cgi-bin/fulltext/110445470/HTMLSTART">http://www3.interscience.wiley.com/cgi-bin/fulltext/110445470/HTMLSTART</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>They perform normal mode analysis for
enzyme/apo-enzyme. Gives brief of preparation for analysis.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Josiah Zayner<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Anirban Ghosh<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, June 29, 2007 1:06
AM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Energy
Minimization Protocol for running Normal ModeAnalysis</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi,<br>
I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. For
that I require a well minimized structure. I have minimized my structure using
steepest descent and conjugate gradient. But the structure seems to have got
struct in a local energy minima. How should I proceed to get a well minimized
structure in order to go for <st1:place w:st="on">Normal</st1:place> mode
Analysis? <br>
Please suggest any protocol.<br>
<br>
Regards,<br clear=all>
<br>
-- <br>
<font color="#000066"><span style='color:#000066'>Anirban Ghosh<br>
<st1:PlaceName w:st="on">M.Tech</st1:PlaceName> <st1:PlaceName w:st="on">Bioinformatics</st1:PlaceName>
<br>
<st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:City w:st="on"><st1:place
w:st="on">Hyderabad</st1:place></st1:City><br>
<st1:City w:st="on"><st1:place w:st="on">Hyderabad</st1:place></st1:City> - 500
046<br>
Andhra Pradesh<br>
<st1:country-region w:st="on"><st1:place w:st="on">India</st1:place></st1:country-region></span></font>
<o:p></o:p></span></font></p>
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