sruiz's blog

How to calculate ROC curves

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.

Small Molecule Dihedrals Parametrization

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).

Gaussian09 bug fix

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)

Gaussian 09 fix

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