<br>Thanks for the Justin's suggestion, I have tried in this way<br>
g_rmsf -f trj.xtc -s .tpr -res -oq .pdb -o .xvg then selected c-alpha<br>
then the b-factor values in .pdb file are seperated by
write programming, result 2 coulmns are generated and plotted the graph
residue vs nm.<br>
Can you tell me the way iam doing whether correct or not? this may be trivial question but i am new to gromacs. <br>
any suggestion would be appreciated.<br><div><span class="gmail_quote"></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br> <br> sudheer babu wrote:<br>
> Hi,<br> > I would like to calculate B-factor of protein, so I performed<br> > command like this<br>
>
g_rmsf -f .xtc -s .tpr
-res -o fluctuate.xvg -od devi.xvg it has<br> > run without error.Now i am bit doubting that which .xvg file have to<br> > take for plot B-factor values?<br> <br>> I think you have not specified the correct options. Check g_rmsf -h and read<br>
> about the -oq option.<br> <br> -Justin<br> <br> > B-factor is nothing but thermal devation of atoms. I think, I should<br> > take dev.xvg for plotting B-factor values, if it is coorect, then what'<br> > s the need for producing fluctuate.xvg? may be this is trivial question.<br>
> Could anyone help me pls.<br> > Thanks alot in advance<br> ><br> ><br> > ------------------------------------------------------------------------<br> ><br> > _______________________________________________<br>
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Graduate Research Assistant<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br> End of gmx-users Digest, Vol 51, Issue 102<br> ******************************************<br> </blockquote></div><br>