VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Sep 25 2023 - 17:13:46 CDT

There is something wrong with those paths with spaces. It's on my list to
fix.
Also, I tried to run the binary manually and I noticed it is not getting
libnetcdf.dylib.

A quick-and-dirty solution is for right now:
#1 libnetcdf.dylib copy it somewhere cionize finds it.
cd '/Applications/VMD 1.9.4a57-arm64-Rev12.app/Contents/vmd'
cp libnetcdf.dylib plugins/MACOSXARM64/bin/cionize1.0

#2 Set the path using { } to prevent spaces from disappearing.
set env(CIONIZEBINDIR) {/Applications/VMD
1.9.4a57-arm64-Rev12.app/Contents/vmd/plugins/MACOSXARM64/bin/cionize1.0}

#3 Run
$env(CIONIZEBINDIR)/cionize -p ...

On Mon, Sep 25, 2023 at 5:07 PM Ropón-Palacios G. <groponp_at_gmail.com> wrote:

> I apologize for the omission of the detail: 1) I have exported as follows
> the PATH of VMD from my zshrc (MacOS Big Sur): export PATH=
> /Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd:$PATH
>
> , 2) the command I use is the following:vmd_MACOSXX86_64 -dispdev text -e
> cionize.tcl
>
> 3) my script contains the following lines:
> package require cionize
> namespace import ::cionize::*
> set id [mol new ../tmp_top.psf type psf waitfor all]
> mol addfile ../tmp_top.pdb type pdb waitfor all
>
> #! Run with a suffcient number of ions to saturate the model
> #! This example estimates 3x magnitude of system net charge
> set charge [expr {round([vecsum [[atomselect top "all"] get charge]])}]
> set number [expr {abs($charge*3)}] ; # 3x magnitude of system net charge
> #! np is the number of procs
> cionize -mol $id -np 4 -mg -ions "{SOD $number 1} {CLA $number -1}"
> #mol delete all
>
> Error:
>
> Starting cionize...
> pqrplugin) Warning no atom radii available, assigning radii of 1.0
> Info) Opened coordinate file cionize-temp.pqr for writing.
> Info) Finished with coordinate file cionize-temp.pqr.
> couldn't find program `/Applications/VMD'
>
> On Monday, Sep 25, 2023 at 6:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> You are not making any sense here and making it extremely difficult to
> give some meaningful advice.
>
> You have to explain in more detail what exactly you did; how and where you
> typed what command and in which order.
> Also, you are not consistent, because what you quoted here is different
> from what you quoted before.
>
>
> On Mon, Sep 25, 2023 at 4:59 PM Ropón-Palacios G. <groponp_at_gmail.com>
> wrote:
>
>> I’m using:
>>
>> export PATH="/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd
>> <https://urldefense.com/v3/__http://1.9.4a57-x86_64-Rev12.app/Contents/vmd__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZWStuIHq$>
>> :$PATH”
>>
>> To fix the error, but donot fix any way for fix it?
>>
>> it error only get when cionize, for other plugin it work fine
>>
>>
>> geo.
>>
>>
>>
>> On Monday, Sep 25, 2023 at 5:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> wrote:
>> This looks a lot like you are using a Tcl script that does not take into
>> account that path names may contain a blank.
>> This more commonly happens on Windows, but obviously applies to your case
>> as well.
>> The equivalent path on your Linux machine probably does not have a blank.
>>
>>
>> On Mon, Sep 25, 2023 at 4:35 PM Ropón-Palacios G. <groponp_at_gmail.com>
>> wrote:
>>
>>> Dear,
>>>
>>> try export all paths, possible from APP vmd :
>>>
>>> export PATH="/Applications//Applications/VMD
>>> 1.9.4a57-x86_64-Rev12.app/Contents:$PATH
>>> <https://urldefense.com/v3/__http://1.9.4a57-x86_64-Rev12.app/Contents:$PATH__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZZhhXTdb$>
>>> "
>>> 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!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZZMVrZjr$>
>>> "
>>>
>>> bet following get again following error:
>>>
>>> Starting cionize...
>>> pqrplugin) Warning no atom radii available, assigning radii of 1.0
>>> Info) Opened coordinate file cionize-temp.pqr for writing.
>>> Info) Finished with coordinate file cionize-temp.pqr.
>>> couldn't find program `/Applications/VMD’
>>>
>>> how can fix it?
>>>
>>> best,
>>>
>>> Geo.
>>>
>>>
>>> On Monday, Sep 25, 2023 at 3:49 AM, Castro Martinez Camila <
>>> camila.castro_at_tu-dortmund.de> wrote:
>>>
>>> Did you add vmd into the path in your macOS?
>>>
>>>
>>> Camila
>>> ------------------------------
>>> *De:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> en nombre de
>>> ROPÓN-PALACIOS G. G. <groponp_at_gmail.com>
>>> *Enviado:* domingo, 24 de septiembre de 2023 13:57:26
>>> *Para:* VMD Mailing List
>>> *Asunto:* vmd-l: <<cionize on macOS error>>
>>>
>>> Dear all, I’m using cionize on my MacOS con last version of VMD (with
>>> bug fixed to OS big surf on 2022) , then I use cionize :
>>>
>>> As document into the protocol of Juan R. Perilla,
>>> https://urldefense.com/v3/__https://link.springer.com/protocol/10.1007/978-1-4939-7756-7_13__;!!DZ3fjg!-h8WaG5FUJ8kYgOQKxtAUcfXY9Kw5lZN_9R7PhJk_n88c-sTkmZVX62MHB6uPsWQgbvV8voXFoRkhB9NZ7U5$
>>> <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!-h8WaG5FUJ8kYgOQKxtAUcfXY9Kw5lZN_9R7PhJk_n88c-sTkmZVX62MHB6uPsWQgbvV8voXFoRkhIVcJH1T$
>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZQsp1zbk$>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>
>>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!-h8WaG5FUJ8kYgOQKxtAUcfXY9Kw5lZN_9R7PhJk_n88c-sTkmZVX62MHB6uPsWQgbvV8voXFoRkhIVcJH1T$
> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZQsp1zbk$>
> College of Science & Technology, Temple University, Philadelphia PA, USA
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu