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Autodock/Vina/MGLTools Installation

posted Feb 9, 2011, 3:47 PM by Dong Xu   [ updated Mar 9, 2013, 9:54 PM ]
by Kevin Wu

On Savor:

   1. Compiled autodock and autogrid from source. All make tests pass, no problems here.
   2. Downloaded vina 32-bit binaries.
   3. Installed Python 2.5.5 for pdb2pqr, installed numpy into this local dir of python.
   4. Fixed readline problem by installing readline-dev and recomplining python. (I think activepython you installed doesn't have the readline error anymore either.)
   5. Compiled pdb2pqr, all tests pass.
   6. Downloaded MGLTools 64-bit binary. Fixed read line errors here by linking libreadline.so.5 to libreadline.so.4.
   7. Added links to of software to /home/lab/apps/bin. pdb2pqr can't be linked beacuse of some python path problems.
   8. NOTE: MGLTools is a little different from when I last used it. You still need to use their install of python, but you dont have to source anything anymore if you put this line into your bashrc (or source their init file):

     alias pythonsh='/home/lab/apps/mgltools_x86_64Linux2_1.5.4/bin/pythonsh'

However you need to run all mgltools scripts with pythonsh prefixed. Ie: pythonsh prepare_ligand4.py .

Install was similar on the beowulf cluster. I added stuff to the bashrc so that everything was ok.


Best solution: If system python has different version, say 2.6, Activepython is 2.7 and MGL python is 2.5
Go in prepare_ligand4.py and add python2.5, therefore, no need to source mglenv.sh everytime
same applies to pdb2pqr.py
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