I will make a short tutorial about how to generate ROC curves and other statistics after running rDock molecular docking (for other programs such as Vina or Glide, just a little modification on the way dataforR_uq.txt file is interpreted will make it work, see below).

I assume all of you are familiar with what ROC curves are, what are they for and how they are made.

We have found ourselves several times in a situation where we have to parametrize compounds for running MDs.
In this blog entry, I will try to set up a protocol for parametrization of small molecules dihedrals for AMBER using Gaussian and sander (based on the tutorial found in this webpage).

Thanks to Jordi, we could find a solution to this gaussian bug: (I wanted to parametrize a compound with iop(6/33=2) which has been deleted in our marc g09 version)

http://ambermd.org/bugfixesat.html



Gaussian 09 fix