Thanks for the Justin's suggestion, I have tried in this way g_rmsf -f trj.xtc -s .tpr -res -oq .pdb -o .xvg then selected c-alpha 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. Can you tell me the way iam doing whether correct or not? this may be trivial question but i am new to gromacs. any suggestion would be appreciated.
> > > sudheer babu wrote: > > Hi, > > I would like to calculate B-factor of protein, so I performed > > command like this > > g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has > > run without error.Now i am bit doubting that which .xvg file have to > > take for plot B-factor values? > > > I think you have not specified the correct options. Check g_rmsf -h and > read > > about the -oq option. > > -Justin > > > B-factor is nothing but thermal devation of atoms. I think, I should > > take dev.xvg for plotting B-factor values, if it is coorect, then what' > > s the need for producing fluctuate.xvg? may be this is trivial > question. > > Could anyone help me pls. > > Thanks alot in advance > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 51, Issue 102 > ****************************************** >
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