[gmx-users] Re: gmx-users Digest, Vol 51, Issue 102

[sudheer babu]

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
> >
> >
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> --
> ========================================
>
> 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
>
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> End of gmx-users Digest, Vol 51, Issue 102
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