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 https://my.vmware.com/web/vmware/free#desktop_end_user_computing/vmware_player/6_0
In alternative, a working 30-days VMware Workstation trial can be downloaded at:
http://www.vmware.com/products/workstation/workstation-evaluation
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 http://www.vmware.com/products/fusion/
Instructions for Software Installation For Linux Users (no VM)
-AmberTools14 (mandatory) and Amber14 (optional, a licence is requested)
For more information see http://jswails.wikidot.com/installing-amber14-and-ambertools14
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 http://ambermd.org/AmberTools14-get.html
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:
cd $AMBERHOME
./configure gnu
(answer "Y" to any question)
make install
Other software needed for the workshop:
OPENEYE
compressed executables for trial versions of OMEGA, ROCS and VIDA will be provided for different architectures.
Linux installation: unpack the .tar.gz file in the installation directory (i.e. /usr/local) and make sure that the bin folder is in your path:
export OPENEYE=/usr/local/openeye
export PATH=$OPENEYE:$PATH
DOCKING SW
PLANTS, SPORE and pharmACOphore can be downloaded from http://www.tcd.uni-konstanz.de/research/plants.php
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 http://autodock.scripps.edu/downloads MGLtools can be downloaded from http://mgltools.scripps.edu/downloads
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 https://www.cgl.ucsf.edu/chimera/download.html ; follow Instructuions provided at the download site)
VMD http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=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: http://jswails.wikidot.com/mac-os-x
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.
OTHER COMMERCIAL PACKAGES:
Maestro (a free academic license can be requested at http://www.schrodinger.com/freemaestro/)
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 http://www.schrodinger.com/downloadcenter/ 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
pkamya[at]chemcomp.com