VMD-L Mailing List

From: Ropón-Palacios G. (groponp_at_gmail.com)
Date: Mon Sep 25 2023 - 17:23:40 CDT

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:
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> Hi Geo,
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> 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:
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> alias vmd='/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/MacOS/startup.command'
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> 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.
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> I hope this helps,
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> Best,
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> Hale
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> 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>>
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> I’m using:
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> export PATH="/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH”
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> To fix the error, but donot fix any way for fix it?
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> it error only get when cionize, for other plugin it work fine
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> geo.
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> > On Monday, Sep 25, 2023 at 5:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com (mailto:akohlmey_at_gmail.com)> wrote:
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> > This looks a lot like you are using a Tcl script that does not take into account that path names may contain a blank.
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> > This more commonly happens on Windows, but obviously applies to your case as well.
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> > The equivalent path on your Linux machine probably does not have a blank.
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> > On Mon, Sep 25, 2023 at 4:35 PM Ropón-Palacios G. <groponp_at_gmail.com (mailto:groponp_at_gmail.com)> wrote:
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> > >
> > > Dear,
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> > > try export all paths, possible from APP vmd :
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> > >
> > > export PATH="/Applications//Applications/VMD 1.9.4a57-x86_64-Rev12.app/Contents:$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$)"
> > >
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> > >
> > > bet following get again following error:
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> > > Starting cionize...
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> > > pqrplugin) Warning no atom radii available, assigning radii of 1.0
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> > > Info) Opened coordinate file cionize-temp.pqr for writing.
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> > > Info) Finished with coordinate file cionize-temp.pqr.
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> > >
> > >
> > > couldn't find program `/Applications/VMD’
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> > > how can fix it?
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> > > best,
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> > > Geo.
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> > > > 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:
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> > > > Did you add vmd into the path in your macOS?
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> > > >
> > > > Camila
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> > > >
> > > >
> > > > 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 :
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> > > >
> > > > 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!-HypaAoHQ01IlDHa002wfOnjASo81KwoAwBF1HakxIqG5MCeJ4HQVmpdolbFCGL-E4h7P5vvnE4h6wYW$ (https://urldefense.com/v3/__https:/link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWBTJoVUW$)
> > > >
> > > >
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> > > > But get the following error : Couldn’t find /Application/VMD
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> > > > It only into macOS because into Linux running normal,
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> > > > Help me please,
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> > > > Best,
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> > > > Geo
> > > >
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> > > >
> > > >
> > > > Enviado de Outlook para iOS (https://urldefense.com/v3/__https:/aka.ms/o0ukef__;!!DZ3fjg!_j39KWGxQzwPpvfsCFoxxiVS_IrO54Gt8mxBLAsi57oaQdQVuhemguHYHvQ1hIePyKnqPKBnWB74AGMQ$)
> > > >
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> > > >
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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!-HypaAoHQ01IlDHa002wfOnjASo81KwoAwBF1HakxIqG5MCeJ4HQVmpdolbFCGL-E4h7P5vvnNk7XKlm$ (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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