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How to install LigBuilder v2.0?


    LigBuilder v2.0 is written in C++ language and has been tested on LINUX platforms.

    Program dependency:

             Please install OpenBabel version 2.3.0 or later first, and make sure the path of babel was added to the system executive path. OpenBabel is not an essential part of the design process, but four functions will be affected if OpenBabel was absence. (Automatic mode, 2D-Clustering, Clustering Reporter, Synthesis Reporter)

             Click here to go to OpenBabel website.

    Database dependency (optional):

             Please obtain at least one commercial available molecules database as the material library of LigBuilder v2.0, e.g. ACD, ZINC, SPECS or other databases which user may gain these entities for synthesis. If material library is absence, LigBuilder will judge the material by some simple experiential rules.

    Support for SVG:

             LigBuilder v2.0 result reporter required the SVG(Scalable Vector Graphics) supported by your browser. If you could not see images in the report page, please install and use one of the following browsers.

                SVG-Supported browser: Google Chrome, Safari, Opera(Version > 8.0), Firefox(Version >1.5), Internet Explore 9, Flock, Camino, SeaMonkey.

    Display resolution (optional):

                Please set your display resolution 1280*1024 or higher to view the reported HTML pages.

    Environment Setting:

             Add following line into ~/.bashrc or ~/.cshrc or ~/.tcshrc.(According to you shell)

             ulimit -s unlimited

                (As the program will call the "babel" directly, please add the path of OpenBabel to the enviroment variable if "babel" is not executable in the working directory. This is not usually necessary if the OpenBabel is installed with root permission.)

             NOTICE: This would NOT take effect in shells opened so far.

             Please relogin current shell before next step.

    Installation of LigBuilder v2.0:

                Unpack the package in a LINUX shell like this:

             tar  -xvf  LigBuilderV2.tar.gz

                Make symbol links by:

             cd LigBuilderV2
             ./configure

    Now a directory named "LigBuilderV2" has been created in your working directory. Under that directory, there are following subdirectories:

    LigBuilder v2.0 has two executive modules, i.e. CAVITY, BUILD.

   Building Material Database (optional):

      (NOTICE: If this step was skipped, LigBuilderV2 will take molecules small than a criterion for material instead of actual molecules. We strongly recommend user to prepare an enormous material database to enhance the speed and accuracy of retro-synthesis)

      Convert your material library file to Mol2 format and set to the corresponding path of the input file "LigBuilderV2/build/material.input". Please notice: user should assign the source or name of the molecule as the title of molecule (e.g. ZINC00018471) if the current title is not recognizable , as LigBuilder v2.0 will use the title to indentify where the material molecule come from. All the valences on these structures must be fulfilled, and hydrogen atoms should be added. Please check the atom types and bond types of your structures carefully, as these information may be lost or changed during format converting.

      Entering the working directory and build database by following commands (default input path is "LigBuilderV2/build/material.mol2"):

             cd LigBuilderV2/build
             ./build -MatDatabase material.input

          

       Now LigBuilder v2.0 is ready, Good luck!


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(These web pages are edited by Yaxia Yuan. Latest update: Jan., 2012)