VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 25 2023 - 15:49:35 CDT

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> wrote:

> Dear,
>
> try export all paths, possible from APP vmd :
>
> export PATH="/Applications//Applications/VMD
> 1.9.4a57-x86_64-Rev12.app/Contents:$PATH"
> export PATH="/Applications//Applications/VMD
> 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH"
>
> 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> wrote:
>
> Did you add vmd into the path in your macOS?
>
>
> Camila
> ------------------------------
> *De:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> en nombre de
> ROPÓN-PALACIOS G. G. <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!8dPNhLoWaZrS2nb4AGjkEKIe2y55vdue38kyA03cVTJp_GDA9pK3rZXM3gNruDF1cEFMWfud3NmokJPQ4w$
> <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  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!8dPNhLoWaZrS2nb4AGjkEKIe2y55vdue38kyA03cVTJp_GDA9pK3rZXM3gNruDF1cEFMWfud3NnmwtjTmA$ 
College of Science & Technology, Temple University, Philadelphia PA, USA