The Molecule Calculator (MolCalc)

Hosted at molcalc.org

Installation

If you want to install it on your own server with PHP support, of course.

Install Dependencies

• PHP5 / Apache2

• OpenBabel w/ PNG Support Make sure that the the correct libs are installed before compile open babel. See above link. If you are using Ubuntu, OpenBabel is install via

    sudo apt-get install openbabel
  

• GAMESS. You must obtain a copy of the GAMESS code separately from their website.

• mod rewrite. MolCalc uses a .htaccess script for redirecting the web requests. Please make sure mod_rewrite is enabled. On ubuntu this is done by running the command

    sudo a2enmod rewrite
  

Installation

• Clone MolCalc

    git clone https://github.com/jensengroup/molcalc.git molcalc
  

  and a new folder is created named 'molcalc'

• Setup MolCalc settings. Copy and paste settings.default.ini to settings.ini in the root folder

    cp settings.default.ini settings.ini
  

  fill in the settings needed

  • tmpfolder: Path to temporary working folder. Must be read/writable by the www-user.

  • rungms: The path to the rungms executable

• Make the "data"-folder in MolCalc root with write rights for www-data

    mkdir data
    chmod 777 data
  

• Check health_check.php via a browser to check if everything is setup correctly.

• Done, Happy Mol-Calculating

GAMESS Note

There might be some issues for some 'rungms' scripts. Note that the MolCalc application will be run default on the www-data user (via apache), and will not have the $HOME variable set for rungms.

My advice is to copy rungms to rungms_molcalc, remove all $HOME variables and use that rungms instead.

Changelog

Changes in 1.3

For Developers

MolCalc uses

• JSmol to edit and visualise the properties of molecules.

• OpenBabel to convert file formats and creation of 2D PNG structures.

• GAMESS for all QM calculations.

and the source is released under the GPL license.

Extend calculations

Please see the source located in the methods folder.

Credits

MolCalc is written by Jimmy Charnley Kromann and Maher Channir, based on an idea by Jan Jensen.

The development of MolCalc is supported by the University of Copenhagen through the Education at its Best Initiative (Den Gode Uddannelse).

FAQ

Setting up OpenBabel

For OpenBabel to work with PNG bindings (which is needed for the nice Calculation List), you will need to install OpenBabel yourself.

Firstly, install the package dependencies. On Ubuntu you will need the following packages

apt-get install libxml2-dev zlib1g-dev libcairo2-dev libeigen2-dev python-dev

Now we can download OpenBabel 2.3.1 and compile

tar zxf openbabel-2.3.2.tar.gz
mkdir build
cd build
cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
make
sudo make install

Now export the path to Python.

export PYTHONPATH=/usr/local/lib:$PYTHONPATH

Read the full installation description here.

Setting up ModRewrite

On ubuntu the command is simply

    sudo a2enmod rewrite

Compiling GAMESS on your server

Please see this guide on how to compile GAMESS.