software:topical:lifescience:autodock

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software:topical:lifescience:autodock [2018/08/24 08:32] (current)
meesters created
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 +====== Molecular Docking with AutoDock ======
 +
 +[[http://​autodock.scripps.edu/​|AutoDock]] is the academic, canonical tool to perform molecular docking experiments. We provide a module ''​tools/​AutoDock''​((As always the version information is omitted. Just loading the module will load the most current version.)).
 +
 +===== Using the wrapper script =====
 +
 +To leverage the task from 1 (or a few) ligands to be screened to several thousand, we provide a wrapper script, which is available as a module:
 +
 +''​bio/​parallel_Autodock''​
 +
 +The code is under version management and hosted [[https://​gitlab.rlp.net/​hpc-jgu-lifescience/​docking|internally,​ here]].
 +
 +<WRAP center round important 90%>
 +The wrapper script will submit a job, it is not intended to be just within a SLURM environment,​ but rather creates one.
 +</​WRAP>​
 +Calling ''​parallel_Autodock -h''​ will display a help message with all the options, the script provides. Likewise the call ''​parallel_Autodock --credits''​ will display credits and a version history.
 +
 +<WRAP center round important 90%>
 +The AudoDock configuration file is important. Without it or with a minor glitch in it, AutoDock will either refuse to run or might not yield meaningful results. We therefore strongly encourage to run a couple of screenings (different ligands / receptors) per configuration on a login node //before launching the wrapper script and producing zillions of error messages whilst wasting time and your productivity.//​
 +</​WRAP>​
 +
 +==== Generating a Parameter File ====
 +
 +The invocation ​
 +
 +<code bash>
 +$ parallel_Autodock --wp > <some file>
 +</​code>​
 +
 +will write a default parameter file to be edited. If pleased with the (numerical) settings, it can be used as is: All entries reading ''<​field>''​ are substituted per run with the macromolecule file prefixes (see below)
 +
 +==== Proceeding ====
 +
 +The script, after loading the module, can then be run like:
 +
 +<code bash>
 +$ parall_Audodoc [options] -P <path to configuration file> <path to ligand directory>​ <path to pdbqt receptor file>
 +</​code>​
 +
 +The script expects all AudoDock map files to be present in the same directory as the receptor file.
 +
 +About Arguments:
 +  * both, the ligand directory and the path to the pdbqt file, are mandatory
 +  * both can be relative paths
 +  * the ligand directory should contain one ligand per file
 +  * ''​-P,​--parameterfile''​ is a mandatory flag and supposed to be a (relative) path to the configuration file
 +
 +The options:
 +  * ''​parallel_Audodock''​ attempts to deduce your SLURM account. This may fail, in which case ''​-A,​ --account''​ needs to be supplied.
 +  * ''​-N,​--nodes''​ allows to reserve more than 1 node (the default). This may speed up the screening.
 +  * ''​-l,​--runlimit'',​ this defaults to 300 minutes. If > 300 the partition will automatically be switched to ''​nodelong''​
 +  * ''​-p,​--partition'',​ the default is ''​nodeshort'',​ no smp-partition should be choosen.
 +  * ''​-t,​--threads'',​ Vina can work in parallel. Please consult the manual. The default is 1.
 +  * ''​-o,​--outdir''​ output directory path (default is the current working directory)
 +
 +The output will be in the output directory.
 +
  
  • software/topical/lifescience/autodock.txt
  • Last modified: 2018/08/24 08:32
  • by meesters