Install DOCK 3

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OBSOLETE.

Here are your instructions to get started with DOCK 3.5.54

OUTSTANDING ISSUES

1. not paranoia will not run, so we have to curate molecule by hand a bit
2. calibrate not copied.
3. launchjobs4.csh does not run
4. rename HETATM, renumber, chain ID, other issues
5. delphi must be installed.
6. private dir must not be distributed
7. hand edit of md4db.csh
8. cp calibrate INDOCK

A. Get and unpack software

1. Download dock3.5.54 source distribution

2. untar. you will see 4 items. dock, dockenv, test and README

  dock - source code and executable
  dockenv - scripts to help with dock
  test - a directory where you can test dock
  README - this file

3. In dock we provide a binary executable in dock/i386/dock

  a copy is also in dockenv/bin/Linux/dock
  this is the version of dock we use
  It should run on any linux, but we used Fedora/Centos/Redhat.
  It has been tested on Ubuntu.


B. Get database


1. You need to download ZINC.

We recommend "lead like" and "fragment like".

  To get these in  DOCK3.5 format, execute the following commands
  mkdir zinc
  cd zinc
   mkdir bysubset
   cd bysubset
  mkdir 1
  chdir 1
  wget http://zinc8.docking.org/subset1/1/all.db.csh
  mv all.db.csh getleadlike.csh
  csh getleadlike.csh
  cd ..
  mkdir 2
  chdir 2
  wget http://zinc8.docking.org/subset1/2/all.db.csh
  mv all.db.csh getfraglike.csh
  csh getfraglike.csh
  cd ..

C. Get and install 3rd party applications

     Essential: dms, delphi
     Strongly recommended: OEChem, chimera, pymol

1. You need a delphi license from Columbia U.

When you have it we can give you our version of delphi, which we know works with DOCK

2. Get and install dms

   as follows:
   wget http://www.cgl.ucsf.edu/Overview/ftp/dms.shar
   sh dms.shar
   cd dms
   make
   sudo make install
   cp `which dms` ~/dockenv/private

3. Get OEChem. Set up a symbolic link in ~dockenv/3rdparty

4. Get Chimera from www.cgl.ucsf.edu

5. Get PyMol from pymol.org

D. Set up local environment

1. create .login as follows

  cd dockenv
  echo setenv DOCK_BASE `pwd`  >> ~/.login
  echo 'source $DOCK_BASE/etc/login ' >> ~/.login

2. Many more local script customizations will probably be necessary.

E. Test

0. If you use paranoia or our paranoia service, then you do not have to check:

- HETATM->ATOM

 remove chain ID
 renumber residues, atoms in protein
 check frame of reference
 for very large proteins, eliminate distant matter to avoid overflows.


1. We provide data to test DOCK 3.5.54.

More data are available from http://data.docking.org/2009/

  Do this:
  cd
  mkdir work
  cd work
  cp -r ~/test/astex85/1M2Z .
  cd 1M2Z
  cp $DOCK_BASE/scripts/Makefile3 Makefile
  make
  # note as currently written, make will send the receptor to our server for protonation.
  # if you do not want this to happen, you must protonate yourself.

2. To dock the lead like set:

   md4db.csh bysubset 1
   cd run.1

3. To combine the results:

   cd run.1
   combine10.csh 1 `pwd`

4. To review the results:

   load 1.new.eel1 into Chimera/viewdock
   or 1.new.mol2 into PyMol


F. Your first new protein

Now that you have ascertained that DOCK is correctly installed and running, it is time to try it on your own protein. Please try to follow our example, here and on our wiki, in order to prepare the protein, and perform the docking. Docking has many pitfalls. If you ask us, we may be able to help you.

Good docking!

-- John Irwin Sept 25, 2009 jji@docking.org