Week 2

The beginning of this week was working on debugging the cutoff code. Segmentation faults are great! It's now working well, and is faster than trying to do all pairs evaluation of non bonded interactions. The next two goals are to set up some test cases for docking and to investigate OPT++. To come up with some initial test cases I took a look at what AutoDock used as test cases. AutoDock uses genetic algorithms to predict the bound conformation of ligands to macromolecules. There is also a package of python scripts called AutoDockTools which are supposed to help prepare the molecules for docking. The first example I looked at was Streptavidin/biotin. I used AutoDockTools on it as described in the included tutorial. Then I ran AutoDock, to my dismay the conformations were fairly way off from the observed docked conformation. After much struggle with AutoDockTools I finally figured out how to get the correct charges, and AutoDock worked great on the example. So for next week: more test cases!

Week: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10