From: Eric A Brenner (
Date: Thu Dec 08 2016 - 17:27:58 CST


I have about 900 pbd files of small peptides that I plan on running in
NAMD. I'm currently at the step of generating PSF files. I wrote a loop in
Tk Console to test it on a handful of them, and it worked fine. When
running it on all of the pdb files using my laptop, the program crashed. I
have access to a supercomputer which I assume I'll have to use. The
interface with the supercomputer is Bash. I ran VMD and got to this

Info) Dynamically loaded 2 plugins in directory:
Info) ~/vmd-1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
vmd >

Can I treat this as the Tk Console? If not, how can I run autopsf on it?
I tried running autopsf on one of my files and it said:

invalid command name "autopsf"

I've done a lot of Googling and looked through the tutorials, but I'm still
unsure what to do. I'm relatively new to computational work, so forgive my

Thank you