Running DOCK: Difference between revisions
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=Running DOCK= | =Running DOCK= | ||
*modify <tt>INDOCK</tt> | *modify <tt>$mud/INDOCK</tt> and set up the desired directory structure – either manually or by running '<tt>md4db.csh bysubset N<sub>1</sub> N<sub>2</sub> Type</tt>', where <tt>N<sub>1</sub></tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N<sub>2</sub></tt> is the number of chunks (i.e., jobs you can run in parallel), and <tt>Type</tt> is the category of library (i.e., bysubset, byvendor, etc). | ||
* if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock. | * if it hasn't been generated by a script, create the file <tt>dirlist</tt>, which conatins the list of the directories (i.e., chunks of the database) that you want to dock. | ||
*if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. | *if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at <tt>test.</tt>. | ||
*take care that the paths to the <tt>.db.gz</tt> files in <tt>split_database_index</tt> do not get too long. If they do, go via links. | *take care that the paths to the <tt>.db.gz</tt> files in <tt>split_database_index</tt> do not get too long. If they do, go via links. | ||
*submit the calculations to the cluster with <tt>$mud/submit.csh</tt> from the directory in which your data (most importantly, <tt>dirlist</tt>) resides. See [[MUD - Michael's Utilities for Docking]] for setting the $mud variable. | *submit the calculations to the cluster with <tt>$mud/submit.csh</tt> from the directory in which your data (most importantly, <tt>dirlist</tt>) resides. See [[MUD - Michael's Utilities for Docking]] for setting the $mud variable. | ||
[[Category:Manual_DOCK]] | [[Category:Manual_DOCK]] | ||
[[Category:Tutorials]] | |||
Latest revision as of 20:32, 8 October 2012
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.