****************************************************************** DockingApp README file ****************************************************************** DESCRIPTION: DockingApp is a user-friendly graphical application for carrying out molecular docking and virtual screening tasks, meant to enable non-experienced users to easily perform such activities and browse the docking results via a three-dimensional visualization. ************************************************************************************************************************************************************ SYSTEM REQUIREMENTS: DockingApp has been developed in Java SE 7. The application is meant to run locally on any major operating system (Linux, Windows and Apple OS X systems) provided that they are equipped with a suitable 64-bit Java Virtual Machine (JVM) and with a 64-bit Java Runtime Environment (JRE) version 1.7 or higher. Packages are available for download for the respective OS. Please note that DockingApp takes advantage of a multi-threading algorithm that may use a number of processor cores available on the system, by creating and running a suitable number of concurrent threads to carry out the docking/virtual screening tasks. It DOES NOT run on a 32-bit OS and/or JVM. Please make sure that you are running the program in a 64-bit environment. DockingApp requires a minimum of 1GB RAM. For virtual screening against a large number of compounds, at least 4GB RAM is recommended. ************************************************************************************************************************************************************ INSTALLATION AND EXECUTION: Windows 64-bit - If you have not done so before, download and install a 64-bit Java Runtime Environment (JRE) version 7 or higher from www.java.com for your operating system. Please make sure that the environment variable JAVA_HOME is correctly set in your system. If everything is setup correctly, launching the following command: "java -version" from a terminal should display the Java version installed on your system. - Download and unpack the corresponding file from http://www.computationalbiology.it/software/DockingApp_Windows_x64.zip. - Run mgltools_win32_1.5.6_Setup.exe to install MGLTools. - Run DockingApp.bat to launch the program. For its first execution, DockingApp will ask for the installation directory of MGLTools (default location: C:\Program Files (x86)\MGLTools-1.5.6) and the number of processor cores to be assigned to the program (default: half of the available virtual cores on the machine). Upon confirming them, use the "Run" menu to choose either Docking (1 vs 1) or Virtual Screening (1 vs many) in order to configure and launch the desired task. ------------------------------------------------------------------------------------------------------------------------------------------------------------ Linux 64-bit - If you have not done so before, download and install a 64-bit Java Runtime Environment (JRE) version 7 or higher from www.java.com for your operating system. Please make sure that the environment variable JAVA_HOME is correctly set in your system. If you have trouble setting it up, please refer to the instructions listed on http://www.computationalbiology.it/software/java.html. If everything is setup correctly, launching the following command: "java -version" from a terminal should display the Java version installed on your system. - Download and unpack the corresponding file from http://www.computationalbiology.it/software/DockingApp_Linux_x64.tar.gz. - Run setup.sh (from a terminal, navigate to DockingApp's directory and then input: ./setup.sh) to install MGLTools. - Run DockingApp.sh (from a terminal, navigate to DockingApp's directory and then input: ./DockingApp.sh) to launch the program. For its first execution, DockingApp will ask for the installation directory of MGLTools and the number of processor cores to be assigned to the program (default: half of the available virtual cores on the machine). Upon confirming them, use the "Run" menu to choose either Docking (1 vs 1) or Virtual Screening (1 vs many) in order to configure and launch the desired task. ------------------------------------------------------------------------------------------------------------------------------------------------------------ Mac OSX 64-bit - If you have not done so before, download and install a 64-bit Java Runtime Environment (JRE) version 7 or higher from www.java.com for your operating system. Please make sure that the environment variable JAVA_HOME is correctly set in your system. If everything is setup correctly, launching the following command: "java -version" from a terminal should display the Java version installed on your system. - Download and unpack the corresponding file from http://www.computationalbiology.it/software/DockingApp_Mac_x64.zip. - Run setup.sh (from a terminal, navigate to DockingApp's directory and then input: ./setup.sh) to install MGLTools. - Run DockingApp.sh (from a terminal, navigate to DockingApp's directory and then input: ./DockingApp.sh) to launch the program. For its first execution, DockingApp will ask for the installation directory of MGLTools and the number of processor cores to be assigned to the program (default: half of the available virtual cores on the machine). Upon confirming them, use the "Run" menu to choose either Docking (1 vs 1) or Virtual Screening (1 vs many) in order to configure and launch the desired task. ************************************************************************************************************************************************************ TROUBLESHOOTING If you encounter issues in displaying the results of Virtual Screening tasks against a large number of compounds, you may need to increase the memory allocated to the Java Virtual Machine for DockingApp. To do so, open DockingApp.bat (Windows) or DockingApp.sh (Linux and Mac OSX) with a text editor and append the following parameter: -XmxNg, where you should replace "N" with the number of gigabytes to allocate to the JVM. For example, to allocate 4GB to the JVM, your execution file should like the following: - Windows, DockingApp.bat start javaw -jar DockingApp.jar -Xmx4g - Linux/Mac OSX, DockingApp.sh java -jar DockingApp.jar -Xmx4g ************************************************************************************************************************************************************ CITING DOCKINGAPP Elena Di Muzio, Daniele Toti, Fabio Polticelli (2016): DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina ************************************************************************************************************************************************************ Please address comments and report bugs to: Fabio Polticelli fabio.polticelli@uniroma3.it Daniele Toti toti@dia.uniroma3.it