VMD-L Mailing List
From: Leah Isseroff Bendavid (leahbd_at_stanford.edu)
Date: Fri May 16 2014 - 11:55:33 CDT
Thank you so much for all of your help! The error I had reported was
indeed when opening the application directly from the Downloads folder.
When I had copied it into the applications folder and opened it from
there, it still crashed, albeit with a different error, so I figured
that when reporting this problem I'd focus only on the first issue. But
Maxim's advice of opening it through Launchpad instead of directly from
the Applications folder seems to have done the trick, and now it loads
up fine. Really can't thank you enough, I am so grateful for your help!
On 5/16/14, 9:27 AM, John Stone wrote:
> Ah, yes, good catch: Starting with recent revs of MacOS, you must
> now drag the VMD application out of the disk image, and put it into a
> folder on your computer before it will be runnable. This is a result of
> security restrictions that have been added in recent revs of MacOS.
> John Stone
> On Fri, May 16, 2014 at 10:56:34AM -0500, Maxim Belkin wrote:
>> Leah, you should start VMD from 'Applications' folder after installing it. Looking at the path:
>>>> /Volumes/VMD-1.9.1 1/VMD 1.9.1.app/Contents/MacOS/startup.command
>> I can assume that you are trying to start VMD without installing it. Although I'm not sure if that can cause for the problem you have, try installing VMD into 'Applications' folder first and then launch it from a 'Launchpad' so that 'Security Center' asks you for a permission to start it. I have just upgraded to 10.9.3 and VMD runs without any troubles.
>> After installing VMD in the 'Applications' folder, you can launch it from a terminal using:
>> /Applications/VMD\ 1.9.1.app/Contents/Resources/VMD.app/Contents/MacOS/VMD
>> On May 16, 2014, at 10:04 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>> Thanks for reporting this. So far as I am currently aware, you
>>> are the only person that has reported this so far. We will look into
>>> it and let you know what we find out. In general, it is wise to avoid
>>> being too eager with applying MacOS X updates, as they have been widely
>>> known break things, and there's not an easy way to revert when these
>>> things happen. In any case, we will see if we can reproduce the problem
>>> here and let you know what we find out. Do you get any error messages
>>> or VMD console output other than what you pasted below? Did it even get
>>> as far as printing the VMD startup messages?
>>> John Stone
>>> On Thu, May 15, 2014 at 06:58:40PM -0700, Leah Isseroff Bendavid wrote:
>>>> I'm trying to download and use VMD on my Macbook Air, Mavericks OSX
>>>> 10.9.3. When I download and run the VMD 1.9.1 binary [ MacOS X OpenGL
>>>> (32-bit Intel x86) (Apple MacOS-X 10.5.x or later)], it seg faults
>>>> immediately upon opening with the following error:
>>>> /Volumes/VMD-1.9.1 1/VMD 1.9.1.app/Contents/MacOS/startup.command: line
>>>> 7: 1881 Segmentation fault: 11
>>>> "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
>>>> This happens with all other versions of VMD as well.
>>>> Is this a known problem of incompatibility with either the Air or OSX
>>>> 10.9? Are there libraries or software that I would need to download first
>>>> to make VMD compatible?
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349