Install DOCK 3 - Revision history

Frodo at 06:41, 13 March 2014

2014-03-13T06:41:18Z

← Older revision		Revision as of 06:41, 13 March 2014
Line 137:		Line 137:
	jji@docking.org		jji@docking.org

	[[Category:~~Install~~]]		[[Category:Sysadmin]]
	[[Category:DOCK]]		[[Category:DOCK 3.6]]

Frodo at 06:34, 14 February 2014

2014-02-14T06:34:44Z

← Older revision		Revision as of 06:34, 14 February 2014
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			OBSOLETE.

	Here are your instructions to get started with DOCK 3.5.54		Here are your instructions to get started with DOCK 3.5.54

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	[[Category:Install]]		[[Category:Install]]
	~~[[Category:DOCK3]]~~
	[[Category:DOCK]]		[[Category:DOCK]]

Frodo at 20:01, 31 October 2013

2013-10-31T20:01:57Z

← Older revision		Revision as of 20:01, 31 October 2013
Line 134:		Line 134:
	Sept 25, 2009		Sept 25, 2009
	jji@docking.org		jji@docking.org

			[[Category:Install]]
			[[Category:DOCK3]]
			[[Category:DOCK]]

Therese: 6 revisions

2012-10-08T20:27:50Z

6 revisions

← Older revision

Revision as of 20:27, 8 October 2012

Frodo: Install DOCK 3.5.54 moved to Install DOCK 3: 3.5.54 was just one version of the DOCK 3 series

2011-05-11T19:21:09Z

Install DOCK 3.5.54 moved to Install DOCK 3: 3.5.54 was just one version of the DOCK 3 series

← Older revision

Revision as of 19:21, 11 May 2011

Frodo: /* OUTSTANDING ISSUES */

2009-10-22T22:37:35Z

OUTSTANDING ISSUES

← Older revision		Revision as of 22:37, 22 October 2009
Line 3:		Line 3:
	= OUTSTANDING ISSUES =		= OUTSTANDING ISSUES =

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


	= A. Get and unpack software =		= A. Get and unpack software =

Frodo: /* 1. You need to download ZINC. */

2009-09-30T20:15:19Z

1. You need to download ZINC.

New page

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

Frodo at 23:19, 25 September 2009

2009-09-25T23:19:07Z

New page

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/subset2/2/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