必要なプログラム

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install emacs
sudo apt-get install pymol
sudo apt-get install g++
sudo apt-get install gfortran
sudo apt-get install python2.7-dev
sudo apt-get install python-numpy
sudo apt-get install gnuplot

ProDy のセットアップ

wget http://pypi.python.org/packages/source/P/ProDy/ProDy-1.4.5.tar.gz
tar xzvf ProDy-1.4.5.tar.gz
cd ProDy-1.4.5
python setup.py build
sudo python setup.py install

VMD

tar xzvf vmd-1.9.1.bin.LINUX.opengl.tar.gz
cd vmd-1.9.1
./configure LINUXAMD64
cd src
sudo make install

FFTW3

wget http://www.fftw.org/fftw-3.3.3.tar.gz
tar xzvf fftw-3.3.3.tar.gz
cd fftw-3.3.3
./configure --enable-float
make
sudo make install

MEGADOCK

wget http://www.bi.cs.titech.ac.jp/megadock/archives/megadock-2.6.tgz
tar xzvf megadock-2.6.tgz
cd megadock-2.6
make
sudo cp megadock /usr/bin

CafeMol: http://www.cafemol.org/download.php

tar xzvf cafemol_2.1.1164.tar.gz
cd cafemol2.1
cd src
make