Ligand preparation - 20170424 - Revision history

Frodo: asd

2024-05-02T18:09:30Z

asd

2017-11-17T22:53:03Z

3 ways to build ligands:

2017-10-05T18:09:54Z

3 ways to build ligands:

2017-10-05T18:09:16Z

3 ways to build ligands:

2017-04-24T23:39:28Z

← Older revision		Revision as of 23:39, 24 April 2017
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	2. Source the dock environment and submits jobs to build ligands for a given smiles file:		2. Source the dock environment and submits jobs to build ligands for a given smiles file:

	:a. create a file with following commands (in this example, the file's name is cmd ):		:a. create a file with following commands (in this example, the file's name is cmd ). See below the explanation of arguments and change them accordingly!:

	setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk		setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk

2017-04-24T23:14:35Z

← Older revision

Revision as of 23:14, 24 April 2017

2017-04-24T23:13:16Z

← Older revision		Revision as of 23:13, 24 April 2017
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	sh $DOCKBASE/ligand/generate/build_database_ligand.sh mysmiles.smi		sh $DOCKBASE/ligand/generate/build_database_ligand.sh mysmiles.smi

	2. Source the dock environment and ~~submit~~ jobs ~~with~~ :		2. Source the dock environment and submits jobs to build ligands for a given smiles file:

	:a. create a file with following commands (in this example, the file's name is cmd ):		:a. create a file with following commands (in this example, the file's name is cmd ):
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	"/nfs/soft/tools/utils/qsub-slice/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \		"/nfs/soft/tools/utils/qsub-slice/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT \
	-l 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh		-l 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh


	:b. run the script with a smiles file:		:b. run the script with a smiles file:

2017-04-24T23:00:08Z

← Older revision		Revision as of 23:00, 24 April 2017
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	-l 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh		-l 100 $1 $DOCKBASE/ligand/generate/build_database_ligand.sh

	:b. run the script:		:b. run the script with a smiles file:

	csh cmd mysmiles.smi		csh cmd mysmiles.smi

2017-04-24T22:59:31Z

← Older revision		Revision as of 22:59, 24 April 2017
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	3. the following is a wrapper script (wrapper_queue_build_smiles_ligand_corina.csh) which ~~braeks~~ up the smiles file and submits it to the queue. Users may find this script gives more control over the "qsub-mr-meta" way although it is less polished.		3. the following is a wrapper script (wrapper_queue_build_smiles_ligand_corina.csh) which breaks up the smiles file and submits it to the queue. Users may find this script gives more control over the "qsub-mr-meta" way although it is less polished.
	#! /bin/csh		#! /bin/csh

2017-04-24T22:58:35Z

← Older revision		Revision as of 22:58, 24 April 2017
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	What does the qsub submit script exactly do?		What does the qsub submit script exactly do?
	-l 100 --> ~~Submit~~ slices of 100 lines per task to run the script build_database_ligand.sh.		-l 100 --> submit slices of 100 lines per task to run the script build_database_ligand.sh.
	-tc 10 --> ~~But~~ run only 10 tasks at any given time.		-tc 10 --> run only 10 tasks at any given time.
	-s $BUILD_ENVIRONMENT --> source the dock environment before each task is run.		-s $BUILD_ENVIRONMENT --> source the dock environment before each task is run.