Install DOCK 3.7
If you do not already have a cluster with middleware, see: So you want to set up a lab.
Now you are ready for the installation
Installing third-party softwares
This section is for building your own databases. If you use ZINC, you do not need OpenEye, Jchem, Corina or AMSOL.)
- OpenEye (OEChem, Omega)
- More information here for OEChem TK
- More information here for Omega
Apply for academic license here
- JChemBase (Chemaxon)
- Definitely need marvin, molconvert, molcharge . . .
- Academic license here
- Corina (here)
- Chimera
- AMSOL
- PYTHON
- numpy
- scipy
- matplotlib
- biopython (this is need for only one or two scripts, beblasti.py )
- virtual environments are very helpful.
- see $DOCKBASE/install/environ/python/requirements.txt for more information.
- RDkit (not required but useful, see $DOCKBASE/install/environ/python/rdkit.sh for help building rdkit.)
- msms (only need for using beblasti.py) see installing msms
The DOCK Environment is a collection of scripts, programs and 3rd party programs.
Our software
Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html
mkdir -p ~/code cd ~/code tar xzf dock37_source.tar.gz ln -s dock-3.7-release DOCK
set up .cshrc (or .bashrc equivalent)
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK set path = ($path $DOCKBASE/bin) setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4 setenv OE_DIR /raid3/software/openeye/current alias pymol ~/pymol/pymol if ( $?PYTHONPATH ) then if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH} endif else setenv PYTHONPATH $OE_DIR/python endif
Test 1: Basic tests
Before you test our software, test that all third party software is correctly installed.
cd ~/$DOCKBASE/test ./third-party-test.sh
This will tell you quick what you forgot to install or if there is any obvious problem with your installation. Once the above works without error, you are ready to test our software.
cd ~/$DOCKBASE/test ./all-test.sh
This should run about 10-30 minutes depending on your hardware. If you can pass the tests without error, congratulations! You are ready to get started with docking: Getting started with DOCK 3.7.
Possible problems and solutions during installation
- OpenEye missing or problem
- Python missing or problem
- AMSOL missing or problem
- Chemaxon missing or problem
- SGE or problem