VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 27 2012 - 15:26:26 CDT

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.