VMD-L Mailing List

From: Tiglath Moradkhan (moradkhantig_at_gmail.com)
Date: Thu Jan 07 2021 - 20:50:52 CST

Hi Jason

I'm not using a folder that doesn't have admin privileges. I created the
folder myself. Maybe the namd-tutorial-files folder is what is creating the
problem? But from what I've read so far in the tutorial, I should be able
to modify the folder.

Thanks

Tiglath

On Thu, Jan 7, 2021 at 6:19 PM Jason Smith <jason_smith_18_at_sfu.ca> wrote:

> Is this on windows? I get these errors if using a folder that windows
> needs admin privileges for such as the default vmd install directory. Try
> moving your working directory to a location you have full file permissions
> for.
>
>
>
> Cheers,
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Tiglath Moradkhan <moradkhantig_at_gmail.com>
> *Sent:* Thursday, 7 January 2021 5:17:22 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Problem with following NAMD tutorial
>
> To the VMD community
>
> I'm trying to work through the NAMD tutorial,
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf but
> I'm unable to run the ubq.png file
> % source ubq.png
> I get the following error message:
> "couldn't read file "ubq.png": no such file or directory".
>
> I don't understand what the issue is because in the command prompt it
> shows that I'm in the 1-1 build directory and when I type dir, I can see
> the ubq.png file. How do I move to the 1-1 build directory in the Tk
> console?
>
> I also tried using the automatic psf builder but I get the following error
> message:
> "couldn't open "1UBQ_autopsf_preformat_glycan.pdb": no such file or
> directory
> couldn't open "1UBQ_autopsf_preformat_glycan.pdb": no such file or
> directory
> while executing
> "open ${basename}_preformat_glycan.pdb r"
> (procedure "preformat_pdb" line 54)
> invoked from within
> "preformat_pdb $currentMol"
> (procedure "::autopsf::aftersels_gui" line 40)
> invoked from within
> "::autopsf::aftersels_gui"
> invoked from within
> ".autopsf.sels.next invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.sels.next"
> (command bound to event)"
>
> I'm guessing that if I use the plugin that I have to delete the default
> topology files that show up in the topology files section and keep the
> required topology file?
>
> As an aside I'm trying to build a lipoprotein particle. Do I have to use
> the topology file "top_all27_prot_lipid_na.inp"?
>
> I would be glad for some help.
>
>
> Thanks
>
> Tiglath
>
>
>