VMD-L Mailing List
From: Eric A Brenner (ericbrenner_at_utexas.edu)
Date: Thu Dec 08 2016 - 17:27:58 CST
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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
- Next message: Wong Li Zhe: "Re: Superimpose"
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- Reply: Peter Freddolino: "Re: Trying to Use AutoPSF on Hundreds of pdb Files"
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