jjuarez's blog

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

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:

Building AMBER 11 and AmberTools 1.5 on MacOS 10.6.8 (Snow Leopard): A command list

To compile AMBER can be a really hard (or at least long) work. Here there is the list of commands that worked for me in my Snow Leopard machine.  I hope this ease the things a little bit for you.
Enjoy ;-)

Book recomendation: Learn Python The Hard Way, 2nd edition

First time I had to manually manipulate more than 10 files I decided that I must learn any programming language... After many fruitless attempts (programming is not in my background at all), one colleague recommended me this book in order to have a first approach to the python world. Despite the title, its  'Wax on, wax of' teaching style makes it very easy to follow and, in my opinion, very appropriate for a complete newbie like me. You can find it online for free at
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