Install DOCK 3.7 - Revision history

Kyle: Update licensing link to the new page

2025-07-10T08:46:04Z

Update licensing link to the new page

← Older revision		Revision as of 08:46, 10 July 2025
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	= Our software =		= Our software =
	Here we install a private copy under a user's account. It is easy to generalize 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		Here we install a private copy under a user's account. It is easy to generalize 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 dock.compbio~~.~~ucsf~~.~~edu~~/~~Online_Licensing/dock_license_application.html~~]
			[https://license.docking.org/application license.docking.org/application]

	mkdir -p ~/code		mkdir -p ~/code

2024-04-19T20:53:36Z

Installing third-party softwares: asdf

← Older revision		Revision as of 20:53, 19 April 2024
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	'''Now you are ready for the installation'''		'''Now you are ready for the installation'''
	= Installing third-party softwares =		= Installing third-party softwares =
	~~Currently needed third party software:~~		This section is for building your own databases. If you use ZINC, you do not need OpenEye, Jchem, Corina or AMSOL.)
	* OpenEye (OEChem, Omega)		* OpenEye (OEChem, Omega)
	** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]		** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]

2019-03-25T19:32:04Z

Installing third-party softwares

← Older revision		Revision as of 19:32, 25 March 2019
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	** Definitely need marvin, molconvert, molcharge . . .		** Definitely need marvin, molconvert, molcharge . . .
	** Academic license [http://www.chemaxon.com/my-chemaxon/my-academic-license/ here]		** Academic license [http://www.chemaxon.com/my-chemaxon/my-academic-license/ here]
	* corina ~~(still?~~)		* Corina ([https://www.mn-am.com/products/corina here])
	* [http://www.cgl.ucsf.edu/chimera/ Chimera]		* [http://www.cgl.ucsf.edu/chimera/ Chimera]
	* AMSOL		* AMSOL

2019-01-10T22:18:06Z

← Older revision		Revision as of 22:18, 10 January 2019
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	If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].		If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].

	'''Now you are ready to the installation'''		'''Now you are ready for the installation'''
	= Installing third-party softwares =		= Installing third-party softwares =
	Currently needed third party software:		Currently needed third party software:

2019-01-10T22:17:38Z

← Older revision		Revision as of 22:17, 10 January 2019
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	If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].~~</br>~~		If you do not already have a cluster with middleware, see: [[So you want to set up a lab]].

	'''Now you are ready to the installation'''		'''Now you are ready to the installation'''
	= Installing third-party softwares =		= Installing third-party softwares =

2019-01-10T21:32:11Z

Installing third-party softwares

← Older revision		Revision as of 21:32, 10 January 2019
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	* AMSOL		* AMSOL
	** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7		** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7
	** [http://comp.chem.umn.edu/amsol/ AMSOL7.1] is need for DOCK 3.7.1. For instruction ~~and patch~~, see [[AMSOL]]		** [http://comp.chem.umn.edu/amsol/ AMSOL7.1] is need for DOCK 3.7.1. For install and path instruction, see [[AMSOL]]
	*PYTHON		*PYTHON
	**numpy		**numpy

2019-01-10T20:17:54Z

Installing third-party softwares

← Older revision		Revision as of 20:17, 10 January 2019
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	* AMSOL		* AMSOL
	** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7		** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7
	** ~~AMSOL7.1 is need for DOCK 3.7.1:~~ [http://comp.chem.umn.edu/amsol/]		** [http://comp.chem.umn.edu/amsol/ AMSOL7.1] is need for DOCK 3.7.1. For instruction and patch, see [[AMSOL]]
	*PYTHON		*PYTHON
	**numpy		**numpy

2019-01-10T20:13:13Z

Installing third-party softwares

← Older revision		Revision as of 20:13, 10 January 2019
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	* JChemBase (Chemaxon)		* JChemBase (Chemaxon)
	** Definitely need marvin, molconvert, molcharge . . .		** Definitely need marvin, molconvert, molcharge . . .
	** Academic license ~~here:~~ [http://www.chemaxon.com/my-chemaxon/my-academic-license/]		** Academic license [http://www.chemaxon.com/my-chemaxon/my-academic-license/ here]
	* corina (still?)		* corina (still?)
	* [~~https~~://www.cgl.ucsf.edu/chimera/ Chimera]		* [http://www.cgl.ucsf.edu/chimera/ Chimera]
	* AMSOL		* AMSOL
	** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7		** A '''modified''' version of AMSOL6.5.3 is required for DOCK 3.5.54, 3.6, and 3.7

2019-01-10T20:12:28Z

Installing third-party softwares

← Older revision		Revision as of 20:12, 10 January 2019
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	** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]		** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]
	** More information [http://www.eyesopen.com/omega here for Omega]		** More information [http://www.eyesopen.com/omega here for Omega]
	Apply for academic license ~~here:~~ [http://www.eyesopen.com/academic]		Apply for academic license [http://www.eyesopen.com/academic here]
	* JChemBase (Chemaxon)		* JChemBase (Chemaxon)
	** Definitely need marvin, molconvert, molcharge . . .		** Definitely need marvin, molconvert, molcharge . . .

2019-01-10T20:11:59Z

Installing third-party softwares

← Older revision		Revision as of 20:11, 10 January 2019
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	** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]		** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]
	** More information [http://www.eyesopen.com/omega here for Omega]		** More information [http://www.eyesopen.com/omega here for Omega]
	Apply for academic license here: [http://www.eyesopen.com/academic]		Apply for academic license here: [http://www.eyesopen.com/academic]
	* JChemBase (Chemaxon)		* JChemBase (Chemaxon)
	** Definitely need marvin, molconvert, molcharge . . .		** Definitely need marvin, molconvert, molcharge . . .