VMD-L Mailing List

From: Tiglath Moradkhan (moradkhantig_at_gmail.com)
Date: Thu Jan 07 2021 - 23:56:24 CST

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> 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> 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
>>
>>
>>