VMD-L Mailing List

From: Isralewitz, Barry (isralewi_at_illinois.edu)
Date: Thu Feb 22 2024 - 09:45:04 CST

Hi Maud.

Thanks much for the details and file.

An additional question: how are you launching VMD on your Mac? Do you double-click the VMD app icon in the Finder, are you typing a command into Terminal, or do you do something else? "Something else"examples: double-clicking on an alias you've made in the Finder, using Spotlight search, using some non-Spotlight launcher like Alfred or Quicksilver.

Cheers,
Barry

On Feb 22, 2024, at 5:50 AM, Maud Jusot <maud.jusot_at_iktos.com> wrote:

Hi again,

I just wanted to add: my colleague didn't make the bug correction but she turned off her computer yesterday and this morning she installed VMD again and it was working without the fix. I suppose when she turned off the computer, an automated update solved the issue.

Cheers,
Maud

On Thu, 22 Feb 2024 at 11:32, Maud Jusot <maud.jusot_at_iktos.com<mailto:maud.jusot_at_iktos.com>> wrote:
Hi Barry,

1) I'm on MacOS Ventura (v13.6.3) but my colleague was on a different laptop on MacOS Sonoma (v14.2.1).
2) I don't remember making any update on my computer between the successful version and the one with the bug. Same for my colleague. But maybe we didn't pay attention to it. And I'm definitely sure I didn't change anything regarding VMD. And both of us tried to reinstall VMD when we realized it was not working anymore and it didn't solve the problem.

I attached the corrected startup.command file. Basically I just added a "/" before the path to make it work.

Let me know if you need any other details.

Cheers,
Maud

On Wed, 21 Feb 2024 at 19:07, Isralewitz, Barry <isralewi_at_illinois.edu<mailto:isralewi_at_illinois.edu>> wrote:
Hello Maud,

Thanks for the bug report. I have two questions:
1) Which version of macOS are you running?
2) Did you make any changes / upgrades to this machine -- including to the VMD bundle directory -- between the most recent successful (unaltered) VMD launch and when you encountered this bug?

  Also, a bonus question: were your colleagues who also encountered this problem using the same machine as you? If not, I'd be interested in the answers to questions 1) and 2) for one or two of them.

And, this request: could you send, as an email attachment , the version of startup.command that fixed the problem for you? I'm not following the differences and line breaks, versus the shipped version, in the edited version that you pasted in your email text.

Cheers,
Barry


On Feb 21, 2024, at 9:24 AM, Maud Jusot <maud.jusot_at_iktos.com<mailto:maud.jusot_at_iktos.com>> wrote:

Hello,

It seems there is a bug when starting VMD (version 1.9.4 on MACOS ARM). It was working fine a few days ago but not anymore and was the same for a few colleagues. When running the application I got the following error:

'''
Applications/VMD\ 1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command<https://urldefense.com/v3/__http://1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command__;!!DZ3fjg!7eKV6NDHVKgBpFKmy1-rNBYefCsakbmti334M2iYaKfy_0ukhZcooTCnmpUVZsZti52RAuUssQ-VuTjDl8sG$> ; exit;
zsh: no such file or directory: Applications/VMD 1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command<https://urldefense.com/v3/__http://1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command__;!!DZ3fjg!7eKV6NDHVKgBpFKmy1-rNBYefCsakbmti334M2iYaKfy_0ukhZcooTCnmpUVZsZti52RAuUssQ-VuTjDl8sG$>

'''

It seems the path is not recognized correctly anymore. To solve it, I simply edit the `startup.command` as follow:
'''
#!/bin/sh # startup.command # This is the script executed by VMDLauncher to actually start VMD. p=`dirname "$0"` /"$p/../Resources/VMD.app/Contents/MacOS/VMD" $* '''

Hope this can help,

Best,
Maud



--
Barry Isralewitz
Theoretical and Computational Biophysics Group
3143 Beckman, University of Illinois at Urbana-Champaign
Work Phone: (217) 300-1988
Email: isralewi_at_illinois.edu<mailto:isralewi_at_illinois.edu>
https://www.ks.uiuc.edu/~barryi









--
Barry Isralewitz
Theoretical and Computational Biophysics Group
3143 Beckman, University of Illinois at Urbana-Champaign
Work Phone: (217) 300-1988
Email: isralewi_at_illinois.edu
https://www.ks.uiuc.edu/~barryi