VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 29 2012 - 08:01:38 CDT

On Thu, Mar 29, 2012 at 6:05 AM, Ban Arn <ban.arn_at_gmail.com> wrote:
> 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.

no surprise, because it makes no sense.

i gave you a proper explanation and a
suggestion how and where to smarten up.
i cannot help you, if you don't pay attention.

this is purely a PEBCAC issue and not
at all a problem of VMD or the ss_plot tool.

axel.

>
>
> 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.
>>
>>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.