Blogs

Installing PyMol from MacPorts

If you install PyMol from MacPorts you may encounter the following: the control window does not work properly  or does not appears at all. You can save a little of Google diving if you make sure to build tcl (whitout core foundations) and tk (without xquartz) BEFORE trying to install pymol. Hence, you can save time if you follow these simple commands:

% sudo port install tcl -corefoundation
% sudo port install tk -quartz
% sudo port install pymol

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.

MIPGen

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).

Gaussian 09 and Antechamber12

I have recently run into some troubles trying to parametrize a ligand with the latest version of antechamber. As Sergi reported recently, the iop(6/33=2) was deleted in the revision b1 of Gaussian and replaced by the new iop(6/50=1) in the later revision c1 (available at CESCA). The fact is that in the AMBER12 guide is not clearly explained how to obtain an AMBER prep file from the new Gaussian output and for me it has being a little jigsaw. I hope this save you some headaches:

Organic solvent boxes

Due to the demand to use the organic/water mixtures published in the MDMix work done in our group, here you can download two preequilibrated boxes:
  • ETAWAT20 (ethanol 20% concentration)
  • ISOWAT20 (isopropanol 20%). 
These boxes are saved in Amber Object File format. Prepared to work with tLeap or xLeap from Amber software.

Parametrize new ligands for AMBER and CHARMM

      For those who need to parametrize new ligands, there is a new alternative VMD pluggin, named Paratool,  to do so. It works for both AMBER and CHARMM, but has been specially designed for the latter one.

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