Difference between revisions of "Running DOCK"

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=Running DOCK=
 
=Running DOCK=
 
    
 
    
*modify <tt>INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running '<tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>', where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).
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*modify <tt>$mud/INDOCK</tt> and set up the desired directory structure &ndash; either manually or by running '<tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>', where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc).
 
* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.
 
* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.
 
*if you plan to use any of John's scripts in the downstream    processing, leave the output file prefixes at <tt>test.</tt>.   
 
*if you plan to use any of John's scripts in the downstream    processing, leave the output file prefixes at <tt>test.</tt>.   

Revision as of 23:58, 20 September 2011

Running DOCK

  • modify $mud/INDOCK and set up the desired directory structure – either manually or by running 'md4db.csh bysubset N1 N2 Type', where N1 is the identifier of the library (1: lead-like; 2: fragment-like), N2 is the number of chunks (i.e., jobs you can run in parallel), and Type is the category of library (i.e., bysubset, byvendor, etc).
  • if it hasn't been generated by a script, create the file dirlist, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.
  • if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at test..
  • take care that the paths to the .db.gz files in split_database_index do not get too long. If they do, go via links.
  • submit the calculations to the cluster with $mud/submit.csh from the directory in which your data (most importantly, dirlist) resides. See MUD - Michael's Utilities for Docking for setting the $mud variable.