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WebMO - Computational chemistry on the WWW
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April 24, 2014
Computational Chemistry Pre-Compiled Binaries for Mac OS X

Pre-compiled binaries of computational chemistry programs can save the time and trouble of obtaining and compiling the program source code.

The binaries discussed on this page have been tested on Mac OS X 10.5.

MOPAC 7

  1. Obtain the MOPAC 7 binary
    MOPAC 7 is public domain and the pre-compiled binary code mopac7.exe.tar.gz can be obtained from the WebMO website
  2. Uncompress MOPAC 7 binary
    Open your download directory in Finder and double-click the mopac7.tar or mopac7.exe.tar.gz file to uncompress mopac.exe. If this does not occur automatically, open a terminal session and uncompress mopac.exe manually
      $ cd {download_dir}
      $ tar xf mopac7.tar
        or
      $ tar xzf mopac7.exe.tar.gz
  3. Install MOPAC 7 binary
    From a terminal session
      $ sudo bash (enter password)
      # mkdir -p /Applications/chemistry/mopac7
      # cd /Applications/chemistry/mopac7
      # cp -p {download_dir}/mopac.exe
      # chown root:admin mopac.exe
      # exit
  4. Configure WebMO to use MOPAC 7 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable Inerface' icon for MOPAC
    • Click the 'Edit Interface' icon to configure the MOPAC interface
    • Edit entries as follows and click Submit
      • Mopac Version: Mopac 7
      • Mopac path: /Applications/chemistry/mopac7/mopac.exe
      • External parameter dir:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration pages
  5. Login as a WebMO user, and run a test job using MOPAC as the computational engine
MOPAC 2009

  1. Request license (free for academic use) from MOPAC 2009 website:
        http://www.openmopac.net/download-c.html
    A license of the form 12345678a12345678 will be sent to you in an email message
  2. Download MOPAC2009 for Macintosh (MOPAC2009_for_Macintosh.zip) from
        http://www.openmopac.net/Download_MOPAC_Executable_Step2.html
  3. Install MOPAC2009 binary
    From a terminal session
    $ cd {download_dir}
    $ mkdir mopac2009
    $ cd mopac2009
    $ unzip ../MOPAC2009_for_Macintosh.zip
    $ sudo bash (enter password)
    # mkdir -p /Applications/chemistry/mopac
    # cd /Applications/chemistry/mopac
    # cp -p {download_dir}/mopac2009/MOPAC2009.exe .
    # chown root:admin MOPAC2009.exe
    # chmod 755 MOPAC2009.exe
    # xattr -d com.apple.quarantine MOPAC2009.exe
  4. Install MOPAC2009 license
    # export MOPAC_LICENSE=/Applications/chemistry/mopac/
    # /Applications/chemistry/mopac/MOPAC2009.exe {license}
    (press {Return} twice, type "Yes", and press {Return} as prompted, which creates the file password_for_mopac2009)
    # exit
  5. Run a test job from the command line
    $ cd ~
    $ mkdir -p test/mopac2009
    $ cd test/mopac2009
    $ cp -p {download_dir}/mopac2009/Example\ data\ set.mop h2co.mop
    $ export MOPAC_LICENSE=/Applications/chemistry/mopac/
    $ /Applications/chemistry/mopac/MOPAC2009.exe h2co.mop
    $ more h2co.out
  6. Configure WebMO to use Mopac 2009 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Mopac
    • Click 'Edit' to configure the MOPAC interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Mopac Version: Mopac 2009
      • Mopac path: /Applications/chemistry/mopac/MOPAC2009.exe
      • External parameter dir:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  7. Login as a WebMO user, and run a test job using MOPAC as the computational engine
  8. MOPAC documentation
    The online manual for MOPAC2007 covers everything in MOPAC2009, except the MOZYME feature designed for linear scaling of larger molecules
GAMESS

  1. Request a copy of the GAMESS binary
    Visit the GAMESS homepage, click "How to get GAMESS", click "obtaining GAMESS", click "I agree to the above terms", enter your email address, choose the pre-compiled distribution for "GAMESS version Mmm DD, YYYY R# for MacOS X", and click "Submit Request". An email with download instructions will be sent to you.
  2. Obtain the GAMESS binary
    Download the pre-compiled binary file appropriate for your CPU, e.g., gamess-OSX.Current.x86-64.tar.gz for a 64-bit x86 processor, using the username "source" and the password in the email message that you received
  3. Safari will automatically uncompress the archive. If not, open a terminal session and uncompress the downloaded file manually
      $ unzip gamess-OSX.Current.x86-64.tar.gz
  4. Install GAMESS binary
    From a terminal session
      $ sudo bash (enter password)
      # mkdir -p /Applications/chemistry
      # cd /Applications/chemistry
      # tar xvf /{download_dir}/gamess-OSX.Current.x86-64.tar
      # chown -R root:admin gamess
  5. Note Mmm DD YYYY version of GAMESS
      # ls gamess/gamess.*.x
  6. Add a symbolic link to the gamess binary
      # cd gamess
      # ln -s gamess.*.x gamess.00.x
      # exit
  7. Configure WebMO to use GAMESS as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable Inerface' icon for GAMESS
    • Click the 'Edit Interface' icon to configure the GAMESS interface
    • Edit entries as follows and click Submit
      • Gamess Version: Mmm DD YYYY
      • Gamess directory: /Applications/chemistry/gamess
      • Gamess binary: gamess.00.x
      • Ddikick binary: ddikick.x
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration pages
  8. Login as a WebMO user, and run a test job using GAMESS as the computational engine
GAUSSIAN 03

  1. Obtain Gaussian 03 binary
    Gaussian 03 is a commercial software product and must be purchased from Gaussian, Inc. Both source code and pre-compiled binary versions of Gaussian 03 are available. Please visit the Gaussian website for information about purchasing a 32-bit or 64-bit binary version of Gaussian 03 for Mac OS X.
  2. Setup gaussian group and add authorized users to this group
    Select Apple: System Preferences...: Accounts
    Click the lock in the lower-left to make changes, and enter an administrator name and password
    Click the + button, select New Account: Group, and enter Name: gaussian
    Click Create Group
    With the gaussian group highlighted, check the user accounts that are permitted to run gaussian, e.g., smith
    Click the lock in the lower-left corner to end making changes
    Add the webserver user (www in OS X 10.4, or _www in OS X 10.5) to the gaussian group. This must be done manually using terminal (Applications/Utilties/Terminal) because the webserver is not an ordinary user.
    In OS X 10.4,
        $ sudo dscl . -merge /Groups/gaussian GroupMembership www
    or in OS X 10.5,
        $ sudo dscl . -merge /Groups/gaussian GroupMembership _www
    Note: group permissions can be verified from terminal with
        $ id -p smith
        $ id -p www
    or
        $ id -p _www
  3. Copy binary distribution from CD-ROM
    Create the new folder /Applications/chemistry
    Insert CD-ROM
    Copy /tar/*.TAZ from CD-ROM into /Applications/chemistry
    Eject CD-ROM
  4. Extract files and change permissions
    Run /Applications/Utilities/Terminal
    $ sudo bash
    # cd /Applications/chemistry
    # tar xzvf *.TAZ
    # chown -R root:gaussian g03
    # exit
  5. Optionally, setup gaussian environment and run a test job from terminal
    $ cd ~
    $ mkdir g03
    $ cd g03
    $ vi g03setup.sh
          export g03root=/Applications/chemistry
          export GAUSS_SCRDIR=/tmp
          source $g03root/g03/bsd/g03.profile
    $ cp -p /Applications/chemistry/g03/tests/com/test001.com test001.com
    $ cp -p /Applications/chemistry/g03/tests/ia64/test001.log test001.log.ia64
    $ source g03setup.sh
    $ g03 < test001.com > test001.log.osx
    $ tail test001.log.ia64
    $ tail test001.log.osx
  6. Configure WebMO to use Gaussian03 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Gaussian
    • Click 'Edit' to configure the Gaussian interface
    • Verify that the first two entries are correct:
      • Gaussian Version: Gaussian 03
      • Gaussian root directory: /Applications/chemistry
    • Click the 'Suggest' button to fill the remining entries
    • Click the 'Submit' button for the changes to take effect
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  7. Login as a WebMO user, and run a test job using Gaussian as the computational engine

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