[gmx-users] automated analysis

[Leonardo Sepulveda Durán]

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
~~~~~~~~~~~~~~~~~~~~~~~~~