From: Ban Arn (ban.arn_at_gmail.com)
Date: Wed Mar 28 2012 - 04:47:27 CDT

Dear All

Thanks for help & suggestions

Balaji

On Tue, Mar 27, 2012 at 9:26 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Mar 27, 2012 at 12:55 PM, Ban Arn <ban.arn_at_gmail.com> wrote:
> > Dear VMD users
> >
> > Recently, I came across the below link and tried to calculate secondary
> > structures for trajectory frames using the tcl script given in the link.
> >
> > link:
> >
> http://nefeli.mbg.duth.gr/cgi-bin/wiki.pl/Secondary_structure_analysis_of_protein_trajectories
> >
> > The script uses vmd for calculation.
> >
> > The first step works fine and i got the output ss_traj.dat.
> >
> > In the second step, it shows that using ss_plot it converts ss_traj.dat
> into
> > post script file.
> >
> > While using command ss_plot <ss_traj.dat> test.ps, i'm getting error as
> > ss_plot command doesnt found.
> >
> > I copied & pasted the source code for ss_plot.c in the working directory,
> > still i'm running out of the same problem.
>
> this is an *elementary* linux/unix problem and not at all
> specific to the calculation. on a (proper) machine, the
> current directory ('.') is not part of the path (unlike on
> Windows and its predecessor DOS) and thus executables
> are not found unless you specify a more qualified path,
> for example ./ss_plot
>
> please have a look at some linux beginner guides for
> more explanations on this issue.
>
> cheers,
> axel.
>
>
> >
> > Kindly advice.
> >
> > Many Thanks
> > Balaji
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>