From: Wayne Dawson (dawson_at_bi.a.u-tokyo.ac.jp)
Date: Thu Jan 07 2010 - 06:44:52 CST

> 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.

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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