VMD-L Mailing List

From: Ropón-Palacios G. (groponp_at_gmail.com)
Date: Mon Sep 25 2023 - 15:59:39 CDT

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!-qFNa-ejcIayg5K1ZbR-lNVnHqr1XcOTMFjwmDQZ-krELu-wqWMCvyUfbPw5P-O1uESGPGP_TMoj5EGT$ (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!-qFNa-ejcIayg5K1ZbR-lNVnHqr1XcOTMFjwmDQZ-krELu-wqWMCvyUfbPw5P-O1uESGPGP_TLFFawyn$
> College of Science & Technology, Temple University, Philadelphia PA, USA