VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 07 2015 - 07:03:19 CST

On Sun, Dec 6, 2015 at 8:39 AM, zeynab hoseyni <zmhoseyni_at_gmail.com> wrote:
>
> ---------- Forwarded message ----------
> From: zeynab hoseyni <zmhoseyni_at_gmail.com>
> Date: Sun, Dec 6, 2015 at 1:39 PM
> Subject: Re: vmd-l: couldn't execute "psfgen": no such file or directory
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
>
>
> Hi Axel,
>
> Thanks for your answer. I've found the psfgen binary file from the
> namd installation files I already downloaded and put it in the same
> directory as that of the make_arm.tcl script. I performed it again:
> sourcing and running the mentioned command within tk console
> but still receiving the same error..
> Do you have any idea what is wrong?

this is just normal behavior on any unix-like operating system. the
current working directory is not part of the search path for
executables (and for good reasons. it is a bad security problem to
have the current working directory have precedence over the PATH
environment).

you have to use an absolute path or adjust your PATH environment
variable. i would expect that the tutorial you are following contains
instructions for that. i suggest you re-read the docs.

also, is there a specific reason that you use these (old) scripts and
not the (newer) nanotube plugin in VMD?

axel.

> All the Best,
> Zeynab
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.