VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Jan 21 2025 - 08:08:27 CST

Hi Stipe,

How did you install VMD? The default VMD installations that you can
download from the ks.uiuc.edu website don't come with a python
interpreter built-in. Instead, if you want python and graphics, you end
up needing to compile VMD yourself.
https://urldefense.com/v3/__https://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLeSGKjP8$
has a blogpost describing the process, and she's also got a way of
installing VMD as a python package (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLw_8HEtI$ ). I've
got packaging instructions for alpha versions of VMD that I use within
my lab as well. https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKL8qbMb2s$

Hope this helps!

-Josh

On 1/20/25 2:18 PM, Stipe Mustać wrote:
> Hello! I am trying to use python interpreter in vmd. The error message
> I keep getting is:
>
> Info) Starting Python...
> 'import site' failed; use -v for traceback
> rlwrap: warning: vmd crashed, killed by SIGSEGV (core dumped).
> rlwrap itself has not crashed, but for transparency,
> it will now kill itself with the same signal
>
> warnings can be silenced by the --no-warnings (-n) option
> Segmentation fault (core dumped)
>
> I saw a person who posted in this mailing list having the same issue
> in 2023, tried to reproduce all the tutorials and guides, but without
> any success. I would appreciate any help.
>
> Sincerely,
> Stipe Mustac
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io