The Molecule Calculator (MolCalc)
Hosted at molcalc.org
If you want to install it on your own server with PHP support, of course.
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
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
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.
Changes in 1.3
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.
Please see the source located in the methods folder.
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).
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.
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.