VMD-L Mailing List

From: Ban Arn (ban.arn_at_gmail.com)
Date: Thu Mar 29 2012 - 05:05:38 CDT

Dear Axel

I tried the run the script ss_plot <ss_traj.dat> test.ps by keeping the
script ss_plot.c in the working directory.

Still, it doesn't wrok.

Kindly advice.

Many Thanks
Balaji

On Wed, Mar 28, 2012 at 10:47 AM, Ban Arn <ban.arn_at_gmail.com> wrote:

> 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.
>>
>
>