From: Andreas Kukol (
Date: Thu Apr 25 2019 - 10:35:16 CDT


I am trying to work though the 1-page QwikMD Glycoside Hydrolase Tutorial and encountered the following problems:

Step 2: Load Glycoside Hydrolase by typing 7CEL
ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0

Fixed this by downloading 7CEL.pdb manually and then browse and load the molecule into QwikMD

Step 2:
Unable to open file /usr/tmp/torplot_temp.pdb for writing
ERROR) Unable to open file /usr/tmp/torplot_temp.pdb of type pdb for writing frames.

I think this is caused by lacking write permission to the /usr folder, but I am not sure how to fix that.

I am using VMD 1.9.3 installed in /home/akukol/vmd-1.9.3 (this is were all the files are) and /home/akukol/bin/ for the startup script. LINUX Kubuntu 18.04

Many thanks