VMD-L Mailing List

From: Tiglath Moradkhan (moradkhantig_at_gmail.com)
Date: Fri Jan 08 2021 - 11:54:58 CST

Hi Jason

It actually was the folder location. When I changed the folder location in
the Tk console, I was able to use the automatic psfgen builder. I didn't
know that I had to do this before using the plugin. However the code in the
NAMD tutorial still doesn't run.

Thanks

Tiglath

On Fri, Jan 8, 2021 at 9:39 AM Jason Smith <jason_smith_18_at_sfu.ca> wrote:

> 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>
> 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
>>>
>>>
>>>