VMD-L Mailing List

From: Hasdemir, Hale Siir (halesh2_at_illinois.edu)
Date: Mon Sep 25 2023 - 17:20:19 CDT

Hi Geo,

I agree with Axel, I cannot pinpoint where you get the error. But in regard to adding VMD to your path, try adding the line below to your ~/.bash_profile:

alias vmd='/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/MacOS/startup.command'

Then, source ~/.bash_profile. With this alias, you should be able to run vmd from terminal by just typing “vmd”. Then, try running your tcl script.

I hope this helps,
Best,
Hale

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ropón-Palacios G. <groponp_at_gmail.com>
Date: Monday, September 25, 2023 at 5:00 PM
To: Axel Kohlmeyer <akohlmey_at_gmail.com>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>, Castro Martinez, Camila <camila.castro_at_tu-dortmund.de>
Subject: Re: vmd-l: Re: <<cionize on macOS error>>
I’m using:

export PATH="/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH”

To fix the error, but donot fix any way for fix it?

it error only get when cionize, for other plugin it work fine

geo.

On Monday, Sep 25, 2023 at 5:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>> wrote:
This looks a lot like you are using a Tcl script that does not take into account that path names may contain a blank.
This more commonly happens on Windows, but obviously applies to your case as well.
The equivalent path on your Linux machine probably does not have a blank.

On Mon, Sep 25, 2023 at 4:35 PM Ropón-Palacios G. <groponp_at_gmail.com<mailto:groponp_at_gmail.com>> wrote:
Dear,

try export all paths, possible from APP vmd :

export PATH="/Applications//Applications/VMD 1.9.4a57-x86_64-Rev12.app/Contents:$PATH<https://urldefense.com/v3/__http:/1.9.4a57-x86_64-Rev12.app/Contents:$PATH__;!!DZ3fjg!-qFNa-ejcIayg5K1ZbR-lNVnHqr1XcOTMFjwmDQZ-krELu-wqWMCvyUfbPw5P-O1uESGPGP_TJoL4Ine$>"
 export PATH="/Applications//Applications/VMD 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH<https://urldefense.com/v3/__http:/1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH__;!!DZ3fjg!-qFNa-ejcIayg5K1ZbR-lNVnHqr1XcOTMFjwmDQZ-krELu-wqWMCvyUfbPw5P-O1uESGPGP_TMTIXeJE$>"

bet following get again following error:

Starting cionize...
pqrplugin) Warning no atom radii available, assigning radii of 1.0
Info) Opened coordinate file cionize-temp.pqr for writing.
Info) Finished with coordinate file cionize-temp.pqr.
couldn't find program `/Applications/VMD’

how can fix it?

best,

Geo.

On Monday, Sep 25, 2023 at 3:49 AM, Castro Martinez Camila <camila.castro_at_tu-dortmund.de<mailto:camila.castro_at_tu-dortmund.de>> wrote:

Did you add vmd into the path in your macOS?

Camila

________________________________
De: 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>> en nombre de ROPÓN-PALACIOS G. G. <groponp_at_gmail.com<mailto:groponp_at_gmail.com>>
Enviado: domingo, 24 de septiembre de 2023 13:57:26
Para: VMD Mailing List
Asunto: vmd-l: <<cionize on macOS error>>

Dear all, I’m using cionize on my MacOS con last version of VMD (with bug fixed to OS big surf on 2022) , then I use cionize :

As document into the protocol of Juan R. Perilla, https://urldefense.com/v3/__https://link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!_Q4jlKafh_NEpH2RPRxKQnkB3fu0gl8rkMfcQ6NMg9t1qWuXWrgi661c2UmOiseXcMi3XXF5z1_4ByQ8Q45cmA$ <https://urldefense.com/v3/__https:/link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWBTJoVUW$>

But get the following error : Couldn’t find /Application/VMD

It only into macOS because into Linux running normal,

Help me please,

Best,

Geo

Enviado de Outlook para iOS<https://urldefense.com/v3/__https:/aka.ms/o0ukef__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWB74AGMQ$>

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Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!_Q4jlKafh_NEpH2RPRxKQnkB3fu0gl8rkMfcQ6NMg9t1qWuXWrgi661c2UmOiseXcMi3XXF5z1_4ByT33PyFbg$ <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!DZ3fjg!-qFNa-ejcIayg5K1ZbR-lNVnHqr1XcOTMFjwmDQZ-krELu-wqWMCvyUfbPw5P-O1uESGPGP_TLFFawyn$>
College of Science & Technology, Temple University, Philadelphia PA, USA