From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Jan 07 2010 - 08:02:37 CST

Dear Wayne,

On Thu, Jan 7, 2010 at 6:44 AM, Wayne Dawson <dawson_at_bi.a.u-tokyo.ac.jp> wrote:
>
>> I think VMD is assuming that you are using the default Terminal
>> application for opening files with the extension ".command". If you've
>> overridden this and set NetBeans to open .command files, and if NetBeans
>> does not behave like Terminal does (ie. it should run the contents of the
>> .command file as a shell script), then it probably won't launch VMD
>> correctly.
>>
>> If that is the problem, you can fix it by creating somefile.command (it
>> can be empty), then do a File:Get info on it, and set the default
>> application for opening the file to Terminal, and tell it to apply that
>> preference to all files with the extension.
>>
> Thank you for the suggestions.
>
>
> I finally found a related post at
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4954.html
>
>
> It seems that "open" is rather unreliable.  They really should have a flag
> for opening a terminal, like what probably happened for the text editor in
> the post above, but they don't.

"open" does have such a flag, actually. Try "open -a Terminal".

Cheers,
Leo

> The only application in the entire /Applications and $HOME directory with
> the name startup.command is there inside of "VMD 1.8.7app".
>
> What I found works ok is to open a terminal and start vmd as an alias
>
>> cat .bash_profile
> #  .....
> alias vmd="/Applications/VMD 1.8.7.app/Contents/MacOS/startup.command"
>
>
> launch  "Terminal.app" and type "vmd".  That works at least.
> Wayne
>
>>
>
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-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign