Thank you Jason for details. Really I was using bash, I will follow these
suggestions.
Regards
Kshatresh
On Sun, Aug 3, 2014 at 11:03 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, Aug 3, 2014 at 2:56 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com
> >
> wrote:
>
> > Dear Users,
> >
> > Sorry for asking a question which may not be appropriate for amber
> > archive. I am following the amber advance tutorial 17 for umbrella
> > sampling. When I am using the script :
> > #!/bin/csh
> > foreach i ( *.dat )
> > echo $i
> > cat $i >> all_dihedrals.dat
> > end
> >
> > It is showing error as
> > script-all-dihed: line 2: syntax error near unexpected token `('
> > script-all-dihed: line 2: `foreach i ( *.dat )'
>
>
> > Please help me to solve this issue, I have no much knowledge of shell
> > scripting.
> >
>
> It is an important skill to learn for people that perform calculations as
> a regular part of their studies. In order for us to tell you what went
> wrong, though, you need to tell us exactly what you did.
>
> The shell script here is written in C-shell (the shebang line, starting
> with #!, indicates that this script is intended to be run with /bin/csh).
> The default shell most people use -- bash -- has a completely different
> syntax compared to C-shell. What Asaminew sent you was the same script
> written in bash. The fact that his script worked meant that however you
> were executing the script (maybe "bash <script>" or "sh <script>") was
> forcibly invoking the bash shell rather than the correct shell (C-shell).
>
> Shell scripting is useful for many purposes -- it helps automate tasks so
> large numbers of tasks can be carried out very rapidly while reducing the
> chance for mistakes. And if you find a mistake, you can fix it and re-run
> the tasks you need re-run instantly. It also serves as a record of
> _exactly_ what you've done, preserving all of the details.
>
> I suggest picking a shell (probably 'bash' since that's what you seem to be
> using), and start scripting your various tasks, consulting Google when you
> don't know how to do something.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Sun Aug 03 2014 - 13:30:03 PDT
