From: Joao Ribeiro (
Date: Fri Apr 26 2019 - 08:57:56 CDT

Hi Andreas,

Again, this issue is solved in the alpha version, and I am not quite sure about what you meant with being a beginner and using the alpha version. Although it is a testing version, it is an improved version of VMD, with a lot of bug fixes, like this one.

On the QwikMD side, did you install the beta version from QwikMD website (


João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851

On 4/26/19, 4:31 AM, "Andreas Kukol" < on behalf of> wrote:

    Dear João,
    The link to the new version of VMD seemed to be the alpha version, so as a beginner I better stick with VMD 1.9.3
    I could not create the \usr\tmp folder as I don't have write permission for that. I tried to define the variable VMDTMPDIR in .vmdrc:
    set env(VMDTMPDIR) /home/akukol/vmdtmp
    and verified in the vmd console that the variable was set. It still did not work.
    Then I tried in .vmdrc: set VMDTMPDIR and finally in my .bashrc: export VMDTMPDIR=/home/akukol/vmdtmp
    But the problem remained: Unable to open file /usr/tmp/torplot_temp.pdb for writing
    Many thanks
>-----Original Message-----
>From: Joao Ribeiro []
>Sent: 25 April 2019 19:32
>To: Andreas Kukol;
>Subject: Re: vmd-l: QwikMD Glycoside Hydrolase Tutorial step 2
>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.
>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
>I hope this help
>João Vieira Ribeiro
>Theoretical and Computational Biophysics Group Beckman Institute, University
>of Illinois
>+1 (217) 3005851
>On 4/25/19, 10:35 AM, "Andreas Kukol" < on behalf
>of> 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