Ligand preparation - Revision history

Frodo at 03:57, 13 March 2014

2014-03-13T03:57:43Z

← Older revision		Revision as of 03:57, 13 March 2014
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	{{Template:CC-BY-SA-30}}		{{Template:CC-BY-SA-30}}
	{{Template:Coleman}}		{{Template:Coleman}}

	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
	[[Category:Internal]]		[[Category:Internal]]
	~~[[Category:Docking]]~~
	[[Category:Software]]		[[Category:Software]]

Frodo at 01:03, 11 March 2014

2014-03-11T01:03:18Z

← Older revision		Revision as of 01:03, 11 March 2014
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	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Docking ~~database~~]]		[[Category:Docking]]
			[[Category:Software]]

Frodo at 02:16, 24 February 2014

2014-02-24T02:16:45Z

← Older revision		Revision as of 02:16, 24 February 2014
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	'''NB ~~this version appears~~ to refer to a version that is local to UCSF'''		'''NB these instructions appear to refer to a version that is local to UCSF and not part of the DOCK 3.7 distribution YET'''

	Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:		Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:

Frodo at 02:16, 24 February 2014

2014-02-24T02:16:12Z

← Older revision		Revision as of 02:16, 24 February 2014
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			'''NB this version appears to refer to a version that is local to UCSF'''

	Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:		Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:
	db2start.e.csh input.smi ref		db2start.e.csh input.smi ref

Frodo at 03:57, 23 February 2014

2014-02-23T03:57:37Z

← Older revision		Revision as of 03:57, 23 February 2014
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	db2end-prefix.py name		db2end-prefix.py name
	To build dockable name-XXXXXX.db2.gz files.		To build dockable name-XXXXXX.db2.gz files.

			This pertains strictly to preparing [[mol2db2]] format files for docking using [[DOCK 3.7]]. Look elsewhere for database preparation for previous versions.


	{{Template:CC-BY-SA-30}}		{{Template:CC-BY-SA-30}}

Frodo at 03:56, 23 February 2014

2014-02-23T03:56:46Z

← Older revision		Revision as of 03:56, 23 February 2014
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	{{Template:Coleman}}		{{Template:Coleman}}
	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
			[[Category:Internal]]
			[[Category:Docking database]]

Frodo at 21:29, 13 February 2014

2014-02-13T21:29:06Z

← Older revision		Revision as of 21:29, 13 February 2014
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	Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:		Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:
			db2start.e.csh input.smi ref
	db2start.e.csh input.smi ref
	Or to build on a standalone machine, use		Or to build on a standalone machine, use
			db2gen.e.csh input.smi ref
	db2gen.e.csh input.smi ref
	Note that many programs must be properly installed and available or this script will fail. The most troublesome is EPIK. For this reason, among others, Dahlia Weiss has helped get Marvin's Chemaxon cxcalc running in lieu of EPIK. This is probably the preferred way to build molecules. Run it on the cluster with:		Note that many programs must be properly installed and available or this script will fail. The most troublesome is EPIK. For this reason, among others, Dahlia Weiss has helped get Marvin's Chemaxon cxcalc running in lieu of EPIK. This is probably the preferred way to build molecules. Run it on the cluster with:
			db2start.e.cxcalc.csh input.smi
	db2start.e.cxcalc.csh input.smi
	The format of the input file here is a two column file with one column being a SMILES string and the other column being an ID. Any length IDs are valid, but only 16 characters will get carried into the DOCKing phase of the operation, see Mol2db2_Format_2 for more details.		The format of the input file here is a two column file with one column being a SMILES string and the other column being an ID. Any length IDs are valid, but only 16 characters will get carried into the DOCKing phase of the operation, see Mol2db2_Format_2 for more details.

	Once the jobs have finished, you can run		Once the jobs have finished, you can run
			db2end-prefix.py name
	db2end-prefix.py name
	To build dockable name-XXXXXX.db2.gz files.		To build dockable name-XXXXXX.db2.gz files.

Frodo: Created page with "Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SM..."

2014-02-13T21:28:45Z

Created page with "Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SM..."

New page

Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:

db2start.e.csh input.smi ref
Or to build on a standalone machine, use

db2gen.e.csh input.smi ref
Note that many programs must be properly installed and available or this script will fail. The most troublesome is EPIK. For this reason, among others, Dahlia Weiss has helped get Marvin's Chemaxon cxcalc running in lieu of EPIK. This is probably the preferred way to build molecules. Run it on the cluster with:

db2start.e.cxcalc.csh input.smi
The format of the input file here is a two column file with one column being a SMILES string and the other column being an ID. Any length IDs are valid, but only 16 characters will get carried into the DOCKing phase of the operation, see Mol2db2_Format_2 for more details.

Once the jobs have finished, you can run

db2end-prefix.py name
To build dockable name-XXXXXX.db2.gz files.

{{Template:CC-BY-SA-30}}
{{Template:Coleman}}
[[Category:DOCK 3.7]]