[gmx-users] automated analysis

[Anthony Cruz]

Thank you all.

This resolve my problem!!

Anthony

On Thursday 15 December 2005 11:34 am, Leonardo Sepulveda Durán wrote:
> Hello!! I have this Scrip in perl, you should changue the $tpr $gro
> and other variables for the names you need.
>
> ## Select an option in a opened GMX program
> sub PR {
>         local($option)=$_[0];
>         print PGRM "$option \n"; # print a option to g_energy
> }
>
> ## RMSD
> open(PGRM, "| g_rms -s $Gro -f $Trr -o $Sufix\_rms.xvg");
>         &PR(1);&PR(1);&PR(1);
> close(PGRM);
>
> ## RGYR
> open(PGRM, "| g_gyrate -s $Gro -f $Trr -o $Sufix\_rgyr.xvg");
>         &PR(1);
> close(PGRM);
>
> ## Accesible solvent Area
> open(PGRM, "| g_sas -s $Tpr -f $Trr -o $Sufix\_sas.xvg");
>         &PR(2);
> close(PGRM);
>
> ## Number of Protein-Protein Hydrogen Bonds
> open(PGRM, "| g_hbond -f $Trr -s $Tpr -num $Sufix\_hbpp.xvg");
>         &PR(1);&PR(1);
> close(PGRM);
>
> ## Number of Protein-Solvent Hydrogen Bonds
> open(PGRM, "| g_hbond -f $Trr -s $Tpr -num $Sufix\_hbps.xvg");
>         &PR(1);&PR(12);
> close(PGRM);
>
> ## RMSF
> open(PGRM, "| g_rmsf -s $Gro -f $Trr -o $Sufix\_rmsf.xvg");
>         &PR(3);
> close(PGRM);
>
> Leonardo
>
> On 12/15/05, Anthony Cruz <acb15885 at uprm.edu> wrote:
> > But in the case of g_rmsd, g_rmsf, and other that I have to select a
> > group or input some options, How I can specify this options in the
> > Scripps.
> >
> > On Wednesday 14 December 2005 12:10 pm, David van der Spoel wrote:
> > > Anthony Cruz wrote:
> > > > Hi User:
> > > > I want to know if is possible to make a script for analysis of a
> > > > trajectory. Where I specify the options I want to use and the script
> > > > make all the rest.
> > >
> > > you have to write the script.
> > >
> > > > Best regards,
> > > > Anthony
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> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~
> Leonardo Andres Sepúlveda Durán
> Biochemist
> Universidad de Chile
> Codigo postal:  752-0249
> ~~~~~~~~~~~~~~~~~~~~~~~~~
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