start:software:topical:lifesciences:molecular_docking:vina

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start:software:topical:lifesciences:molecular_docking:vina [2021/01/29 16:55]
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-====== Screening the binding of Lingands with Autodock Vina ====== 
- 
-Screening / docking lingand binding with [[http://vina.scripps.edu/index.html|Autodock Vina]] can be done one molecule at a time. We provide a module ''bio/AutoDock_Vina/''((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_Vina''  
- 
-The code is under version management and hosted [[https://gitlab.rlp.net/hpc-jgu-lifescience/docking|internally, here]]. 
- 
-<callout type="warning" icon="true"> 
-The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one. 
-</callout> 
-Calling ''parallel_Vina -h'' will display a help message with all the options, the script provides. Likewise the call ''parallel_Vina --credits'' will display credits and a version history. 
- 
-<callout type="warning" icon="true"> 
-The Vina configuration file is important. Without it or with a minor glitch in it, Vina 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.// 
-</callout> 
- 
-The script, after loading the module, can then be run like: 
- 
-<code bash> 
-$ parall_Vina [options] -C <path to configuration file> <path to ligand directory> <path to pdbqt file> 
-</code> 
- 
-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 
-  * ''-C,--configfile'' is a mandatory flag and supposed to be a (relative) path to the configuration file 
- 
-The options: 
-  * ''parallel_Vina'' 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. A good rule of thumb is to divide the number of ligands by 64 * the number of nodes. This should yield number in the range of 10 (greater than 4, smaller than 12). 
-  * ''-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) 
-  * ''--timeout'' sometimes Vina does not converge, in which case it might be sensible to define a timeout (in seconds), to abort individual Vina runs, such that other ligands can be screened. 
- 
-The output will be in the output directory. There will be 3 files: 
-  * the SLURM output with a prefix composed of the ligand prefix and the target prefix. 
-  * a file called ''energies.csv'' -- results will be written listing the ligand prefix, the target prefix, the affinity of the first Vina output entry, as well as the connected rmsd-values and a time stamp. In case no result was retrieved, the respective rows contain ''NA,NA,NA''. 
-  * a compressed tarball with all vina results, called ''docking_results.tar.gz'' 
- 
-The ''energies.csv'' file allows for quick sorting and filtering, e.g. to retrieve the 10 best hits: 
- 
-<code bash> 
-$ sort -k3 -t',' -r energies.csv |grep -v NA| head 
-</code> 
- 
-Particular hits can be extracted from the tar file: 
-<code bash> 
-$ tar -zxvf docking_results.tar.gz <desired prefix>.pdbqt 
-</code> 
-where the "desired prefix" is the one listed in the ''energies.csv'' or a downstream analysis as shown. 
- 
-===== Downstream Analysis ===== 
- 
-==== Downstream Analysis with Autodock ==== 
- 
-For a downstream analysis with our [[:start:software:topical:lifesciences:molecular_docking:autodock|AutoDock wrapper]], you can use something like the following snippet (or a more sophisticated selection scheme). Be sure that you replace the '-n12' with the desired molecule count. You could also apply an affinity threshold: 
- 
-<code bash> 
-$ # we assume a new directory for autodock ligands 
-$ autodock_ligand_dir="some_path" 
-$ # this is where our ligands, screened with Vina, are stored 
-$ vina_ligand_dir="some_path" 
-$ # link the best n-results to the new Autodock input directory location: 
-$ for prefix in $(tail -n+2 energies.csv| sort -k3 -t',' -r |grep -v NA| head -n12 |cut -f1 -d',' ); do 
-> ln -s ${vina_ligand_dir}/${prefix}.pdbqt ${autodock_ligand_dir}/${prefix}.pdbqt 
-> done 
-</code>