Getting started with DOCK 3.7

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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 bargain for for-profits) at http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html. Request DOCK 3.7.

cd
mkdir code
cd code
cp ~xyz/DOCK.tgz . # or get distro from dock.compbio.ucsf.edu website as above
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

  • run be_blasti
  • run blastermaster


Perform your first fine tuned docking run

In this docking run, we are going to make adjustments from the default protocol in several areas:

  • the docking spheres or hot-spots
  • the vdw grids
  • the electrostatics grids
  • the size of the box
  • a zinc ion and its coordinating residues


Get a pre-prepared library

DOCK 3.7 uses a format new to this version of DOCK called [mol2db2 format]]. It will be available via the normal channels in ZINC. You can of course also prepare your own version locally. As of this writing, you can currently get pre-prepared subsets of lead-like and fragment-like from our server (details to go here).


Return to DOCK 3.7.