Setting up AutoDockTools utility scripts
This How-to applies to:
This How-to is intended for: User
If you installed MGLTools using one of our latest standalone installers, then you are all set. If you are using older version of MGLTools or installed it using binary tarballs, then you need to do some additional steps before you can run these scripts. Here is how.
ADT utility scripts are located in MGLToolsPckgs/AutoDockTools/Utilities24 folder and start with something like:
This tells your shell to use python when running ADT scripts. Unless you installed MGLTools from source, python from your system does not know where to find MGLTools packages, and chances are that you'll get ImportError. The following FAQ shows how to fix this problem:
An alternative solution is to replace python from the first line with $MGL_ROOT/bin/pythonsh. For instance:
Linux version of MGLTools includes two new scripts, mglenv.csh and mglenv.sh located in MGLTools-$Version/bin folder. If you source these files, then you don't need to modify ADT scripts or call them with pythonsh in front.
> source mglenv.csh
> source mglenv.sh
Note that, you need to source for environment variables to remain in effect.
Mac OS X users and others can create mglenv as described here.
Ubuntu/Debian users who installed ADT using
apt-get install autodocktools can find these scripts in /usr/share/pyshared/AutoDockTools/Utilities24. Please use python2.5 interpreter instead of python2.6 which is system default python on Ubuntu 9.04.
- Where can I find the Python scripts for preparing and analysing AutoDock dockings?
- I've read about the Python prepare scripts like "prepare_dpf4.py" in places like the virtual screening tutorial. This FAQ answers the questions, "Which Python scripts are available?", "Where do I download the Python scripts from?" and "Where are these Python scripts installed?".