VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 26 2012 - 05:52:09 CST

On Mon, Nov 26, 2012 at 11:44 AM, Albert <mailmd2011_at_gmail.com> wrote:
> hello:
>
> I am trying to run a python script by command:
>
> vmd npt.pdb md.xtc -python -dispdev text -e count_water.py
>
> but it said:
>
>
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback

you are missing the matching python runtime installation.

> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> ValueError: vmdnumpy module not available.
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "VMD", line 12, in <module>
> NameError: name 'AtomSel' is not defined
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File "/soft/vmd-1.9.1/lib/vmd/scripts/python/Tkinter.py", line 59, in
> <module>
> import _tkinter # If this fails your Python may not be configured for Tk
> ImportError: No module named _tkinter
>
>
> I checked that I've already installed both numpy and tkinter in my Linux OS.

that is irrelevant. you need the packages matching those
that were used to compile VMD. to have a VMD installation
that uses your system python installation you need to
compile VMD from source.

... or rewrite your python script in Tcl.

axel.

> thank you very much
> Albert 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.