Week 8

I finished up the minimization using the "fake" bond and bond angle terms. It works pretty well, but there are still slight changes in the bonds and bond angles. David worked on trying to minimize in dihedral space, although there seems to be some trouble with it.

We have temporary Sybyl licenses so that we can find the partial charges of the atoms. I started working with it to develop some test cases. It's interface is pretty awful, and trying to figure out to simple things like center the molecule are difficult. Autodock has a webpage up describing the Sybyl commands to add hydrogens and find partial charges. The first example I tried was Trypsin and Benzamidine (3ptb) which is the example that comes with autodock. It should be a simple, straightforward example, right? Wrong! The charges and hydrogens are different than the autodock example. They also don't come up with the correct docked structure if run through Autodock. Hopefully I'll be able to figure out what's wrong next week.

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