1

I have recently shifted from Linux to Mac OS. I have installed vmd in this new machine. The vmd just load without any molecule when I type the following:

vmd protein.gro

This *.gro file contains a protein molecule. I want to open this file like in Linux:

*applicationname filename*

But it doensnt work. Launching the molecule via vmd just simply doesnt work. I have tried to google this problem but I couldnt find the right answer. Is there anybody who had the same problem and was able to tackle it ?

PythonNoob
  • 139
  • 2
  • 7

3 Answers3

2

Probably a little late but anyway. You only need to add a line to your bash_profile file.

The bash_profile file is located in: 

/Users/user-name/.bash_profile

(remember to change user-name to your real username and note the dot at the beginning of the file's name)

inside the .bash_profile (or .profile) file add:

alias vmd='csh /Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command.csh'

(for a different version of VMD you will need to change the number (1.9.3) in the path to your actual VMD version). Save and close.

After this just source your .bash_profile (or .profile) file again so the changes are incorporated to your shell or just open a new terminal window.

Now you can type:

vmd my-gro-file.gro

just like in Linux.

gudok
  • 4,029
  • 2
  • 20
  • 30
kbr85
  • 1,416
  • 12
  • 27
1

Is vmd a native Mac app? If so, you should be able to use open -a /path/to/vmd.app filename.

Gordon Davisson
  • 118,432
  • 16
  • 123
  • 151
1

I think it depends on the application itself, but maybe try this. First, find where the application is installed using the Terminal like this:

which vmd

and you should get the path to it. Then use the path like this:

open -a /path/to/vmd --args someMolecule.gro
Mark Setchell
  • 191,897
  • 31
  • 273
  • 432