Dear Justin,<br><br>Thanks for your reply. Well, to explore the effect of the ligand on protein<br><br>g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg<br>Select a group: 1<br>Selected 1: 'Protein'<br>
Select a group: 13<br>Selected 13: 'LİGAND'<br><br><span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">Does</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">this</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">choice</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">make sense</span><span class="" title="Alternatif çevirileri görmek için tıklayın">?</span></span><br>
<br><br><div class="gmail_quote">30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
<br>
I want to see the effect of the ligand on each residue using the following command:<br>
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res<br>
<br>
Select group(s) for root mean square calculation<br>
Select a group: ?<br>
Which group should I choose?<br>
<br>
</blockquote>
<br></div>
The group that is most meaningful to you, based on the behavior observed in the trajectory. You can analyze backbone, sidechain, or all protein atoms separately. Several iterations may be informative, using several different groups.<br>
<br>
-Justin<br>
<br>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>