From: Axel Kohlmeyer (
Date: Mon Dec 07 2015 - 07:03:19 CST

On Sun, Dec 6, 2015 at 8:39 AM, zeynab hoseyni <> wrote:
> ---------- Forwarded message ----------
> From: zeynab hoseyni <>
> 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 <>
> 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

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?


> All the Best,
> Zeynab

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.