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3D Visualizing Quantum Chemistry Molecule in Ubuntu Edgy

Posted January 16th, 2007 by sugree

First of all, I'm not a chemistry scientist at all. It is not my field. This era, we are on the globalization and multi-disciplinary interaction. I am just a computer engineer and any fields might involve to computer. Actually, computer itself is absolutely useless as long as you don't have applications to run. Recent drugs are officially recovered using virtual screening technology based on computational science where as computer system is used as a key component to simulate the effect of each drug candidate instead of going to try it in real laboratory. This technique is a part of quantum chemistry. Not only simulation is used here but also visualization is another critical part. I can't remember how to explain the structure of a molecule but I'm sure it must be in 3D plane. Human may imagine how it is but it is impossible to communicate to others by just description. The only way to solve this problem is 3D visualization in computer. That's why I'm here. Moreover, my box is Ubuntu Edgy. I have to find my way to visualize input/output in 3D.

The main tool we used for quantum chemistry here is GAMESS. It is available in various platform. I definitely don't know what it does to the input file and what it produces in output files. Actually, I would like to see what is in input file but I don't find any visualization tool yet. The one I found is MacMolPlt which is capable to import GAMESS .DAT, open GAMESS .log, open GAMESS .irc and output GAMESS .inp.

In Ubuntu Edgy, MacMolPlt is not there. I have to compile it myself as follows.

  1. Install libwxgtk2.6-dev

    sudo apt-get install libwxgtk2.6-dev

  2. Download MacMolPlt

    wget http://www.scl.ameslab.gov/~brett/MacMolPlt/download/wxMacMolPlt-6.2.0.tar.gz

  3. Extract

    tar xzvf wxMacMolPlt-6.2.0.tar.gz

  4. Run configure

    cd wxMacMolPlt-6.2.0
./configure --prefix=/usr/local

  5. Compile

    make

  6. Install

    make install

All done. Now you are able start MacMolPlt by:

wxMacMolPlt

Then try to open samples/sample.irc and samples/water.log to see how it goes. If you don't see anything, just simple go to menu Edit -> Global Preferences and click Factory Default for all categories. By this step, you will see something in the window.

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