Getting started with DOCK 3.7
Jump to navigation
Jump to search
You want to install DOCK 3.7 on your own system. These are the notes I made while doing it. These are just recommendations, based on my experience. You are free to simply download the software and experiment!
Acquire 3rd party software
- Recommend Centos 6.3 or higher, but other unixes should work
- python 2.7 series - We do not support the 3.x series, and 2.6 or earlier can also cause problems.
- amsol - for database building
- omega / OpenEye - for database building
Acquire our software
Here we are installing a private copy under a single user account. It is easy to change this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a deal for companies!) at http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html. You want to request DOCK 3.7.
cd mkdir code cd code cp ~xyz/DOCK.tgz . # or get distro from dock website tar xzf DOCK.tgz # unpack
set up .cshrc (or .bashrc)
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK setenv SOFT /raid3/software setenv ENV_PYTHON "$SOFT/python/bin/python-env.csh 2.7" source $ENV_PYTHON set path = ($path $DOCKBASE/bin)
Test the installation using the built-in test scripts
cd $DOCKBASE/test ./all-test.sh
Perform your first docking with pre-prepared files
cd mkdir -p docking/test1 cd $DOCKBASE/test/data/xiap/proteins/initial cp rec.pdb xtal-lig.pdb ~/docking/test1/ cd ~/docking/test1/ blastermaster.py -v
Perform your first database generation, using endogenous human metabolites
cd mkdir -p database/testa cd database/testa wget http://zinc.docking.org/db/byvendor/hmdbendo/hmdbendo_p0.smi.gz gunzip hmdbendo_p0.smi.gz *dbgen.csh
Perform your first docking from PDB code alone using be_blasti
Perform your first fine tuned docking run
Get a pre-prepared library
Return to DOCK 3.7.