VMD-L Mailing List

From: Ropón-Palacios G. (groponp_at_gmail.com)
Date: Mon Sep 25 2023 - 16:24:51 CDT

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 (mailto: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 (mailto: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):$PATH__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZXzLa3fw$ ”
> >
> > 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!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 (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!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZU69wPYh$ (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!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZQsp1zbk$
> > > College of Science & Technology, Temple University, Philadelphia PA, USA
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com (mailto:akohlmey_at_gmail.com) https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4zE44QfVy3klbjhH_tUSDA-pG-a0UEqvufR1KDGY_dgAB2XPLnVrxnxrTaf2-qf6XUdGSLRnZQsp1zbk$
> College of Science & Technology, Temple University, Philadelphia PA, USA