Install DOCK 3
Here are your instructions to get started with DOCK 3.5.54
- 1 OUTSTANDING ISSUES
- 2 A. Get and unpack software
- 3 B. Get database
- 4 C. Get and install 3rd party applications
- 5 D. Set up local environment
- 6 E. Test
- 7 F. Your first new protein
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
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.
0. If you use paranoia or our paranoia service, then you do not have to check:
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.
-- John Irwin Sept 25, 2009 email@example.com