Running DOCK

modify INDOCK and set up the desired directory structure – either manually or by running mksdir3.csh 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.

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