3D Visualizing Quantum Chemistry Molecule in Ubuntu Edgy
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
.DAT, open GAMESS
.log, open GAMESS
.irc and output
In Ubuntu Edgy, MacMolPlt is not there. I have to compile it myself as follows.
sudo apt-get install libwxgtk2.6-dev
tar xzvf wxMacMolPlt-6.2.0.tar.gz
cd wxMacMolPlt-6.2.0 ./configure --prefix=/usr/local
All done. Now you are able start MacMolPlt by:
Then try to open
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.