From: Peter Freddolino (
Date: Thu Dec 08 2016 - 19:58:04 CST

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 interface:
> ...
> 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