Dear Justin,<br><br>I used -res flag with the following command but I get<span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps"></span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">pairs</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">of values</span></span> in the output files. is there any mistake related with the command I used?<br>
g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res <br><br><br><br><div class="gmail_quote">2011/5/29 <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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">Quoting ahmet y?ld?r?m <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>:<br>
<br>
</div><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin,<br>
<br>
You said " You can get a per-residue RMSD by using g_rmsf -od to see the<br>
effect of the ligand on each residue."<br>
1. Can you explain the difference between what goes into the -o file, and<br>
what goes into the -od file?<br>
</blockquote>
<br></div>
The -o output is RMSF; the -od output is RMSD.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2. How should I create a index file to see the effect of the ligand on each<br>
residue? Do I have to create the index file?<br>
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg<br>
Is this command sufficient to see the effect of the ligand on each residue?<br>
</blockquote>
<br></div>
An index file should not be necessary. By default, the output is per atom, so use the -res flag if you want the measurements averaged over all atoms in each residue. The command is sufficient to measure the RMSD per residue. Whether or not that is sufficient is up to you.<br>
<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">
3. Furthermore, can you suggest the other analysis tools to see the effect<br></div>
of the ligand *on protein*?<br>
<br>
</blockquote>
<br>
You should identify the quantities you wish to measure, then read in the Gromacs manual about the different utility programs available. You'll learn far more that way.<br>
<br>
-Justin<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
<br>
2011/5/28 <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Quoting ahmet y?ld?r?m <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>:<br>
<br>
Dear users,<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
I want to investigate *Ligand effect *on the protein .<br>
To investigation the interaction of protein-ligand:<br>
*RMSD calculations:*<br>
1.<br>
a) RMSD of Backbone<br>
b) RMSD of Backbone+ligand<br>
2.<br>
a) RMSD of Protein<br>
b) RMSD of Protein+ligand<br>
3.<br>
a) RMSD of Protein-H<br>
b) RMSD of Protein-H+ligand<br>
Which one would you recommend ( 1., 2., and 2.choice)?<br>
<br>
<br>
</blockquote>
Unless the effect of your ligand is very large (i.e., the whole protein is<br>
significantly more or less stable in the presence of the ligand), then<br>
likely none of these analyses will be particularly illustrative as they are<br>
not very sensitive to small changes. You can get a per-residue RMSD by<br>
using g_rmsf -od to see the effect of the ligand on each residue.<br>
Otherwise, the most common quantity measured is backbone RMSD.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</blockquote>
<br>
<br>
<br>
--<br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br>
<br>
<br>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>