From: Eric A Brenner (
Date: Thu Dec 08 2016 - 20:14:13 CST


Thanks for the reply. I should have been more clear about the program
'crashing'. I meant that VMD freezes, and I have to force close it. I
wasn't using mol delete, so I'll make sure to change that!



On Dec 8, 2016 7:56 PM, "Peter Freddolino" <> wrote:

Dear Eric,
You should in fact be able to run autopsf on plenty of files on your
laptop. You don’t give any details with ‘the program crashed’ to help
troubleshoot, but my guess is that you ran the machine out of memory by not
deleting the molecules after you were done with them (by using mol delete),
and thus they accumulated in memory. The situation won’t be much better on
the login node of a supercomputer, which isn’t all that much more powerful
in most cases than a decent workstation.

The vmd prompt that you got will accept commands like the tkcon. Try running
module load autopsf

and then things should work. But I do not recommend doing this on a
supercomputer login node — they’re not designed for heavy lifting, and
you’re likely to hack off the local admins.


> On Dec 8, 2016, at 6:27 PM, Eric A Brenner <> wrote:
> Hi,
> 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 ignorance.
> Thank you
> -Eric