Adventures in Computational Chemistry

There are many softwares available for carrying out molecular docking calculations. Many of these softwares are paid, while some of them are free. AutoDock is one such freely available software. Earlier, there was AutoDock 4.0 version available. One of the problem with the software was the space it would occupy, if you attempt to do multi docking. Recently, there is another algorithm made available under autodock. It is called AutoDock Vina. This is more efficient, robust and fast algorithm. There are many tutorials available to learn AutoDock Vina including: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf and also a video tutorial http://vina.scripps.edu/tutorial.html    But for some reason, few changes or explanation in little detail is always required to make it understandable for a beginner to follow.  Here is a protocol designed in our group, which our Master's student follow to get acquainted to Molecular Docking s