Autodock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. <\/p>\n
The following versions are installed on the CSF:<\/p>\n
Autodock Vina is the new version and can run in parallel (unlike Autodock4). Autodock4-MP is a parallelized version of Autodock4 but should be considered experimental on the CSF. Users are encouraged to try Autodock Vina first.<\/p>\n
Access to Autodock4 and Autodock Vina is not restricted. However users must abide by the license terms of the software and provide citations in publications.<\/p>\n
Please see the Autodock4 license<\/a> (GPL v2) and the Autodock Vina license<\/a> (a permissive Apache license).<\/p>\n To access Vina you must first load the modulefile:<\/p>\n or, for serial autodock4:<\/p>\n For parallel autodock4 load one<\/em> of the following modulefiles:<\/p>\n Any dependent modulefiles will be automatically loaded for you.<\/p>\n The The The Please do not run Autodock on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Note: Autodock4 will not run in parallel (see Autodock MP below).<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n We recommend running the Autodock4 MP version’s serial compilation to give you a set of result against which you can compare the parallel version (see below for how to run in parallel). Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n To see the complete list of command-line flags simply run Note that the OpenMP (multithreaded) version uses the same command-line flags as the above serial version with the addition of a The seed_type<\/em> accepted values are:<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Note that the MPI version (multi-node) uses a different<\/em> set of command-line flags to the above two examples. It requires the following options in the order given here<\/em>:<\/p>\n where<\/p>\n Note that in this version the MPI ranks are single-threaded.<\/li>\n Refer to the paper Multilevel Parallelization of AutoDock 4.2<\/a> for further information for these runtime options and for details on the parallelization strategy and performance improvements.<\/p>\n We have received the following advice from a CSF user who has tested autodock4_mpi:<\/p>\n Assuming you are running the job from the scratch<\/em> directory, the following files should be placed there:<\/p>\n This will output a To run the For further information see the tutorial<\/a> on the AutoDock website. Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n where the path of the docking_base_directory<\/em> and the status_directory<\/em> should be the directory where all the files have been saved (scratch<\/em> in our example).<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Once autodock4 has run, it will generate:<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Autodock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. The following versions are installed on the CSF: Autodock4 v4.2.5.1 Autodock4-MP v4.2.2.1 Autodock Vina v1.1.2 Autodock Vina is the new version and can run in parallel (unlike Autodock4). Autodock4-MP is a parallelized version of Autodock4 but should be considered experimental on the CSF. Users.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1704","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1704","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=1704"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1704\/revisions"}],"predecessor-version":[{"id":3235,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1704\/revisions\/3235"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=1704"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Set up procedure<\/h2>\n
\r\nmodule load apps\/intel-12.0\/autodock\/vina-1.1.2\r\n<\/pre>\n
\r\nmodule load apps\/intel-12.0\/autodock\/4.2.5.1\r\n<\/pre>\n
\r\nmodule load apps\/intel-12.0\/autodock\/4.2.2.1-MP-omp # Single node multithreaded\r\nmodule load apps\/intel-12.0\/autodock\/4.2.2.1-MP-mpi # Single-node MPI\r\nmodule load apps\/intel-12.0\/autodock\/4.2.2.1-MP-mpi-ib # Multi-node MPI\r\n<\/pre>\n
4.2.2.1-MP-omp<\/code> modulefile provides a version that can be used on single Intel compute nodes (up to 24 cores). This also provides a serial version of Autodock4 MP which can be used to verify results from the parallel versions. It is highly recommended you do this to ensure the parallel versions are producing the results you expect!<\/p>\n4.2.2.1-MP-mpi<\/code> modulefile provides a version that can be used on single compute node (up to 24 cores) using MPI.<\/p>\n4.2.2.1-MP-mpi-ib<\/code> modulefile provides a version that can be used across multiple InfiniBand-connected Intel nodes and hence uses fast networking. The number of cores must be a multiple of 24 and the minimum number of cores is 48. This is the recommended MPI version.<\/p>\nRunning the application<\/h2>\n
Autodock4 Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\nautodock4 -p macro.dpf\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Autodock Vina Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\n# NSLOTS will be set to 1, use it to inform vina how many CPUs we requested\r\nvina --cpu $NSLOTS --receptor file1 --flex file2 --ligand file3 -out outfile\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Autodock Vina Parallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe smp.pe 8 # Number of cores (2-24 permitted)\r\n\r\n# NSLOTS will be set to 8 (in this case), use it to inform vina how many CPUs we requested\r\nvina --cpu $NSLOTS --receptor file1 --flex file2 --ligand file3 -out outfile\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Autodock4 MP Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\nautodock4_serial -p macro.dpf\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
autodock4_serial<\/code> on the login node without any input file.<\/p>\nAutodock4 MP Parallel batch job submission (multithreaded)<\/h3>\n
-r<\/code> option for the seed type (if unspecified the default_seed is used):<\/p>\n\r\n-r seed_type<\/em>\r\n<\/pre>\n
\n
same_seed<\/code> – Use a hard-coded seed value, useful only in doing performance measurements by deterministically running the docking.<\/li>\ndefault_seed<\/code> – Use the time of day plus the threadid for the seed.<\/li>\n<\/ul>\n\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe smp.pe 8 # Number of cores (max 24) in a single node\r\n\r\n# You MUST set this to inform autodock how many cores to use:\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\nautodock4_omp -p macro.dpf -l macro.dlg # Send output to logfile macro.dlg\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Autodock4 MP Parallel batch job submission (multi-node)<\/h3>\n
\r\ndocking_list_file docking_base_directory status_directory seed_type map_file_usage<\/em>\r\n<\/pre>\n
\n
\n
same_seed<\/code> – Use a hard-coded seed value, useful only in doing performance measurements.<\/li>\ndefault_seed<\/code>– Use the time of day plus the threadid for the seed.<\/li>\nunique_node_seed<\/code>– Use the time of day plus the threadid plus the MPI rank for the seed.<\/li>\n<\/ul>\nreuse_maps<\/code> or reload_maps<\/code>.<\/li>\n<\/ul>\nFurther Advice on Running MPI Jobs<\/h3>\n
\n
receptor.pdbqt<\/code> – to be read by autogrid4.py<\/code>, a script that can be downloaded from the AutoDock website. It must be run before the autodock4_mpi<\/code> job to have the grid map files previously generated (see below).<\/li>\nfile.gpf<\/code> – file you use to create the grid map files. Take into account that if you reload the grid maps, all the gpf files used must be also in that directory.<\/li>\nligand_receptor<\/em>.dpf<\/code> – a file you create with the prepare_dpf4.py<\/code> script that is available on the CSF by doing:\n\r\nmodule load apps\/binapps\/mgltools\/1.5.6\r\n$ADTUTILS\/prepare_dpf4.py -l ligand<\/em>.pdbqt -r receptor<\/em>.pdbqt\r\n<\/pre>\n
ligand_receptor<\/em>.dpf<\/code> file by default.\n<\/li>\n<\/ul>\nautogrid4<\/code> command to generate grid map files run:<\/p>\n\r\nmodule load apps\/intel-12.0\/autodock\/4.2.5.1\r\nautogrid4 -p sample.gpf -l sample.glg\r\n #\r\n # This will also read the receptor.pdbqt file\r\n<\/pre>\n
\nYou will also need to create the following directories using the mkdir<\/code> command in your scratch<\/em> area (we assume you are running from your scratch<\/em> area):<\/p>\n\n
etc\/<\/code> (here one must save a docking.list<\/em> file with a list of all the names of the ligands. The UsingAutoDock4forVirtualScreening_v4.pdf tutorial can help to know how to create it)<\/li>\nresults\/pdbqt_lip_rules\/<\/code> (inside the pdbqt_lip_rules\/<\/code> directory one must save all the ligands.pdbqt<\/code> files)<\/li>\n<\/ul>\n\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe orte-24-ib.pe 48 # Run on faster IB-connected h\/w (multiple of 24 cores)\r\n\r\n# $NSLOTS is automatically set to the number of cores given above\r\nmpirun -np $NSLOTS autodock4_mpi docking_list_file docking_base_directory \\\r\n status_directory seed_type map_file_usage<\/em>\r\n\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
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Further info<\/h2>\n
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Updates<\/h2>\n