eCheminfo 2014 Oxford Workshop Software

Instructions for Virtual Machine installation with pre-installed Software (Windows and Linux users)
Drug Discovery 2014 Software Download

Ubuntu 64 bit virtual machines (VM) with preinstalled software, available to participants of Drug Discovery Design Methods & Applications workshop, Oxford UK.

To run virtual machines on Windows 64 bit or Linux 64 bit architectures you can download and install the free VMWARE player at

In alternative, a working 30-days VMware Workstation trial can be downloaded at:

Note to Windows 32 bit users: a 32 bit Linux VM will be available with the following preinstalled software:
AmberTools13, PLANTS/SPORE/pharmACOphore, autodock/vina, pymol, vmd-1.8.7, chimera-1.9

Windows versions of OpenEye and Schrodinger software need to be installed under the native operating system.

Note to Mac Users: Ubuntu 64 bit VM can also be run under MAC. You will need to download and install a 30-days free trial of VMWARE FUSION available at

Instructions for Software Installation For Linux Users (no VM)

-AmberTools14 (mandatory) and Amber14 (optional, a licence is requested)

For more information see

a) install necessary packages; for Ubuntu (other distribution might use different syntaxes) type:
sudo apt-get install build-essential flex bison tcsh gfortran g++ xorg-dev libbz2-dev libopenmpi-dev openmpi-bin python-tk python-dev python-matplotlib python-numpy python-scipy libtool patch

b) download AmberTools14 from

c) extract AmberTools14.tar.bz2 to /usr/local/ (needs root privileges) or to any other directory (if root privileges are missing).

d)  set the AMBERHOME environment variable:
export AMBERHOME=path_to_amber14 (i.e. export AMBERHOME=/usr/local/amber14)

e) compile:
./configure gnu
(answer "Y" to any question)
make install

Other software needed for the workshop:

compressed executables for trial versions of OMEGA, ROCS and VIDA will be provided for different architectures.

Linux installation: unpack the .tar.gz file in the installation directory (i.e. /usr/local) and make sure that the bin folder is in your path:
export OPENEYE=/usr/local/openeye

PLANTS, SPORE and pharmACOphore can be downloaded from

Linux installation:
unpack the tarball, change file permissions (i.e. chmod ugo+x PLANTS) and place the executable in your binary path (i.e. /usr/local/bin or /home/bin)

Autodock and autodock vina can be downloaded from MGLtools can be downloaded from

Linux installation (Autodock):
unpack the tarballs, locate the executables in the directory tree, change file permissions (i.e. chmod ugo+x autodock4) and place the executable in your binary path (i.e. /usr/local/bin or /home/bin)

Linux installation (MGLtools):
change file permissions (i.e. chmod ugo+x mgltools_Linux-x86_64_1.5.6_Install), execute as root (i.e. sudo ./mgltools_Linux-x86_64_1.5.6_Install) and follow the instructions.

Recomended software:
openbabel (Ubuntu installation: sudo apt-get install openbabel)
pymol (Ubuntu installation: sudo apt-get install pymol)
chimera (downloadable at ; follow Instructuions provided at the download site)
VMD ; uncompress, cd in the vmd directory, run ./configure, cd in the src directory and run "make install" as root )

for MAC users: detailed instruction to install and compile AmberTools and Amber are available at:
We suggest the use of Ubuntu 64 VM with VMWARE FUSION

for Windows users: compiling Amber software under windows might be quite an headache. We suggest the use of Ubuntu 64 VM with VMWARE PLAYER.


Maestro (a free academic license can be requested at

Schroedinger Suite (click on this link for the License Retrieval Assistant) is specifically needed for Workshop activity and needs a request for a free trial; go to to create an account and download the Schrodinger_Suites_2014-2 package for your architecture.

Download Installation Guide for Schrödinger Software Release 2014-2

a. download >> Schrödinger installation guide for LINUX <<
b. download >> Schrödinger installation guide for MAC <<
c. download >> Schrödinger installation guide for WINDOWS <<

MOE: (suggested, but not mandatory) For a free trial and more information on CCG's academic offering, please contact:
Dr. Petrina Kamya
+1 (514) 393 1055