VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 25 2023 - 16:04:06 CDT

You are not making any sense here and making it extremely difficult to give
some meaningful advice.

You have to explain in more detail what exactly you did; how and where you
typed what command and in which order.
Also, you are not consistent, because what you quoted here is different
from what you quoted before.

On Mon, Sep 25, 2023 at 4:59 PM Ropón-Palacios G. <groponp_at_gmail.com> wrote:

> I’m using:
>
> export PATH="/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd:
> $PATH”
>
> To fix the error, but donot fix any way for fix it?
>
> it error only get when cionize, for other plugin it work fine
>
>
> geo.
>
>
>
> On Monday, Sep 25, 2023 at 5:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> This looks a lot like you are using a Tcl script that does not take into
> account that path names may contain a blank.
> This more commonly happens on Windows, but obviously applies to your case
> as well.
> The equivalent path on your Linux machine probably does not have a blank.
>
>
> On Mon, Sep 25, 2023 at 4:35 PM Ropón-Palacios G. <groponp_at_gmail.com>
> wrote:
>
>> Dear,
>>
>> try export all paths, possible from APP vmd :
>>
>> export PATH="/Applications//Applications/VMD
>> 1.9.4a57-x86_64-Rev12.app/Contents:$PATH"
>> export PATH="/Applications//Applications/VMD
>> 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH"
>>
>> bet following get again following error:
>>
>> Starting cionize...
>> pqrplugin) Warning no atom radii available, assigning radii of 1.0
>> Info) Opened coordinate file cionize-temp.pqr for writing.
>> Info) Finished with coordinate file cionize-temp.pqr.
>> couldn't find program `/Applications/VMD’
>>
>> how can fix it?
>>
>> best,
>>
>> Geo.
>>
>>
>> On Monday, Sep 25, 2023 at 3:49 AM, Castro Martinez Camila <
>> camila.castro_at_tu-dortmund.de> wrote:
>>
>> Did you add vmd into the path in your macOS?
>>
>>
>> Camila
>> ------------------------------
>> *De:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> en nombre de
>> ROPÓN-PALACIOS G. G. <groponp_at_gmail.com>
>> *Enviado:* domingo, 24 de septiembre de 2023 13:57:26
>> *Para:* VMD Mailing List
>> *Asunto:* vmd-l: <<cionize on macOS error>>
>>
>> Dear all, I’m using cionize on my MacOS con last version of VMD (with bug
>> fixed to OS big surf on 2022) , then I use cionize :
>>
>> As document into the protocol of Juan R. Perilla,
>> https://urldefense.com/v3/__https://link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!58Bl2tlhi6suoVQsAbjRFWep1kl_EeZxSwNd_dIMnceTQ7DS7l-fkKXluGbrJS5Jpi4sGzvpwwDg_MQMpg$
>> <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!58Bl2tlhi6suoVQsAbjRFWep1kl_EeZxSwNd_dIMnceTQ7DS7l-fkKXluGbrJS5Jpi4sGzvpwwBe0RVk9g$
> College of Science & Technology, Temple University, Philadelphia PA, USA
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!58Bl2tlhi6suoVQsAbjRFWep1kl_EeZxSwNd_dIMnceTQ7DS7l-fkKXluGbrJS5Jpi4sGzvpwwBe0RVk9g$ 
College of Science & Technology, Temple University, Philadelphia PA, USA