Using minimization/scoring script in Windows

Using minimization/scoring script in Windows

Postby johnkang » Sat Dec 04, 2010 7:17 pm

This post will cover using David's minimization/scoring Perl script to work under your personal computer using Windows 7, but the same principles should apply to earlier versions of Windows. If the server is not loaded, then it may be easier to just use the server minimization/scoring.

1. Make sure you've installed Python, AutoDock and AutoDockVina as described in the instructions. I used Python 2.5 and David used Python 2.6...apparently this may not work for Python 2.7. If you installed AutoDockTools, it should have installed Python 2.5 automatically.

2. Download David's Perl script (viewtopic.php?f=3&t=16). Open the script in your text editor of choice (I recommend Notepad++). Change line 8 $SCRIPTPATH="/usr0/local..." to your AutoDockTools Utilities24 directory. For example, I use
Code: Select all
$SCRIPTPATH="c:/Apps/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/";
. While you're editing, you should make the quick change suggested by David to add hydrogens to the minimization process in order to match the server minimization algorithm (viewtopic.php?f=2&t=25).

3. Download and install a Perl installation for Windows. I used Strawberry Perl. http://strawberryperl.com/

4. Download and install OpenBabelGUI for Windows http://openbabel.org/wiki/Get_Open_Babel. Download and install the Python module for Open Babel http://openbabel.org/docs/2.3.0/UseTheL ... ython.html. Note: I had to right-click->"run as Administrator" for the Python extension in order to install without errors.

5. Next, you'll need to add environmental path variables to your installations. To do this Start button->right click Computer->Properties->Advanced system settings->Advanced->Environmental variables. Under "User variables for YourUsername", edit the PATH variable or create a PATH variable if it does not exist. Make sure there are paths for OpenBabel, strawberryperl, Python, and AutoDockVina. I had to add the paths for Python and AutoDock Vina....the paths to OpenBabel and strawberryperl were auto-generated for me. For example, my PATH variable is (the Firefox part was probably there before and you can ignore it):
Code: Select all
C:\Program Files (x86)\Mozilla Firefox;C:\Apps\OpenBabel-2.3.0;C:\strawberry-perl-5.12.1.0-64bit\c\bin;C:\strawberry-perl-5.12.1.0-64bit\perl\site\bin;C:\strawberry-perl-5.12.1.0-64bit\perl\bin;C:\Python25;C:\Apps\AutodockVina
. You'll also need Python-specific environmental variable called PYTHONPATH in the "user variables for YourUsername" which points to your autodocktools packages directory. For me, PYTHONPATH is
Code: Select all
C:\Apps\MGLTools-1.5.4\MGLToolsPckgs
.


6. Now you should be ready to run David's script. Make sure the perl script, your pdbqt receptor file, and your anchorquery "query_results.sdf" file are all in the same directory. Then navigate to the directory using the Command Prompt (easy way is to shift-right-click some empty whitespace in the directory using Windows Explorer and select "Open command window here"). Then type
Code: Select all
perl dockscore.pl RECEPTOR.pdbqt query_results.sdf minimized_score.sdf
and hit enter. Hopefully it will run smoothly.

7. Go to the class project webpage and submit the minimized_score.sdf and it will select your most negative score.

I'm writing this by memory after just getting it to work so ideally I didn't leave anything out but please e-mail me/post if there are errors. kang.john@medstudent.pitt.edu.
johnkang
 
Posts: 5
Joined: Mon Nov 15, 2010 2:34 pm

Return to Helpful Hints - Fall 2010

Who is online

Users browsing this forum: No registered users and 1 guest

cron