VMD-L Mailing List

From: Ropón-Palacios G. (groponp_at_gmail.com)
Date: Mon Sep 25 2023 - 17:32:31 CDT

Dear all, this cionize error report was fixed with the help of . I have now performed it and run it in the command line: vmd_MACOSXX86_64 -dispdev text -e cionize.tcl

, and it ran. Additionally, I had to set it in my zshrc.:
export PATH=/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH

without use “”

Best all,

and thanks Axel

Geo.

> On Monday, Sep 25, 2023 at 7:23 PM, Me <groponp_at_gmail.com (mailto:groponp_at_gmail.com)> wrote:
> However, I have a lot of systems to prepare, so doing it manually could be really tedious. Is there a way to use the executable and run it like a script?
>
>
> Geo
>
> > On Monday, Sep 25, 2023 at 7:20 PM, Hasdemir Hale Siir <halesh2_at_illinois.edu (mailto:halesh2_at_illinois.edu)> wrote:
> >
> > 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:$PATH”
> >
> >
> >
> >
> >
> >
> >
> >
> > To fix the error, but donot fix any way for fix it?
> >
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> >
> > it error only get when cionize, for other plugin it work fine
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> > geo.
> >
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> > >
> > > On Monday, Sep 25, 2023 at 5:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com (mailto:akohlmey_at_gmail.com)> wrote:
> > >
> > >
> > >
> > > This looks a lot like you are using a Tcl script that does not take into account that path names may contain a blank.
> > >
> > >
> > >
> > > This more commonly happens on Windows, but obviously applies to your case as well.
> > >
> > >
> > >
> > > The equivalent path on your Linux machine probably does not have a blank.
> > >
> > >
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> > >
> > >
> > > On Mon, Sep 25, 2023 at 4:35 PM Ropón-Palacios G. <groponp_at_gmail.com (mailto:groponp_at_gmail.com)> wrote:
> > >
> > >
> > > >
> > > > Dear,
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > try export all paths, possible from APP vmd :
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > export PATH="/Applications//Applications/VMD 1.9.4a57-x86_64-Rev12.app/Contents:$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!9Vix3LLLz4c2wzLkrgFjp7c-l2lFnHK5D-97a7SjQ581HgqmELZdBe25B_QEPk6t1B1hY18GxM4wLCVC$ (https://urldefense.com/v3/__https:/link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWBTJoVUW$)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > But get the following error : Couldn’t find /Application/VMD
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > It only into macOS because into Linux running normal,
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Help me please,
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Best,
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Geo
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Enviado de Outlook para iOS (https://urldefense.com/v3/__https:/aka.ms/o0ukef__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWB74AGMQ$)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich. Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte den Absender und vernichten Sie diese Mail. Vielen Dank.
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> > > > >
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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!9Vix3LLLz4c2wzLkrgFjp7c-l2lFnHK5D-97a7SjQ581HgqmELZdBe25B_QEPk6t1B1hY18GxEBX9HhI$ (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
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