VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Apr 25 2019 - 13:31:40 CDT

Dear Andreas,

Thank you for reporting the error. In fact, old versions of QwikMD (and VMD) had issues with Ubuntu due to the missing "/usrt/tmp/" folder. These and other issues were corrected in the new versions of VMD, which I would recommend to use. https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

If some reason you don't want to update VMD, you can create the folder manually, or direct VMD to an existing folder to be used as a temporary folder by defining the variable env(VMDTMPDIR) in the .vmdrc file.

Again, the new versions of VMD have more updates and fixes than just this one.

There is also an updated version of QwikMD (QwikMD beta) that you can install. Please download QwikMD beta from http://www.ks.uiuc.edu/Research/qwikmd/.

I hope this help

Best

João

 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_illinois.edu
+1 (217) 3005851

On 4/25/19, 10:35 AM, "Andreas Kukol" <owner-vmd-l_at_ks.uiuc.edu on behalf of a.kukol_at_herts.ac.uk> wrote:

    Hello,
    
    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
    Andreas