VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Fri Jan 08 2021 - 11:39:55 CST

Hi,

can you please let us know what the issue was, if it wasn't the folder location? Might come in handy for someone else.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: Tiglath Moradkhan <moradkhantig_at_gmail.com>
Sent: Thursday, 7 January 2021 9:56:24 PM
To: Peter Freddolino
Cc: vmd-l_at_ks.uiuc.edu; Jason Smith
Subject: Re: vmd-l: Problem with following NAMD tutorial

I found out what the issue was. Thanks for the help.

Thanks

Tiglath

On Thu, Jan 7, 2021 at 7:10 PM Peter Freddolino <petefred_at_umich.edu<mailto:petefred_at_umich.edu>> wrote:
Perhaps check the file extension on the psfgen script. It is not an image file.
Best,
Peter

On Thu, Jan 7, 2021 at 10:06 PM Jason Smith <jason_smith_18_at_sfu.ca<mailto: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<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Tiglath Moradkhan <moradkhantig_at_gmail.com<mailto:moradkhantig_at_gmail.com>>
Sent: Thursday, 7 January 2021 5:17:22 PM
To: vmd-l_at_ks.uiuc.edu<mailto: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