Installation

Installation of LCModel GUI

Installing LCModel in Oscar

Installing LCModel in Oscar for personal use is a simple process. Because LCModel has a graphical interface, you will need to connect to Oscar using the Desktop Application via OpenOnDemand, this will make sure we are using a node that can find its $DISPLAY.

0. Connecting to Oscar

Connecting via Desktop App in Open on Demand

  • Visit https://ood.ccv.brown.edu

  • Click on the Desktop Icon and start a Desktop job. If you receive an error the error you are already running a Desktop session, you will need to click on "My interactive sessions" at the top panel on the page. You will see your existing session. Click Launch to start this session.

  • Launch a terminal inside the Desktop interface.

1. Download LCModel tar under your HOME

# change directory to your HOME 
cd ~

2. Download LCModel binaries and uncompress file

# download LCModel
wget http://s-provencher.com/pub/LCModel/programs/lcm-64.tar -O lcm-64.tar
# un-tar file
tar xf lcm-64.tar

3. Run the installer script

./install-lcmodel

At this point a GUI window will pop as follows:

Press Continue. A test report should show up as follows:

Close the result window. A new success window will follow

Finally, you can Exit LCMgui

You may see the following error message: Infiniband hardware address can be incorrect! Please read BUGS section in ifconfig(8). This should not have any effect. It is a known message in Oscar that will go away in a future update

4. Install the License

LCModel is now free. However, you'll need to create an empty license file. You can do so from the terminal as follows. 

cd ~/.lcmodel
touch license

If you have used LCModel before and have an outdated license file, please remove it

5. Copy the Basis Set

cp -r /oscar/data/bnc/shared/lcmodel/basis-sets ~/.lcmodel/basis-sets

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