Running DOCK - Revision history

Therese: 7 revisions

2012-10-08T20:32:23Z

7 revisions

← Older revision

Revision as of 20:32, 8 October 2012

Mysinger: /* Running DOCK */

2011-09-20T23:58:46Z

Running DOCK

← Older revision		Revision as of 23:58, 20 September 2011
Line 1:		Line 1:
	=Running DOCK=		=Running DOCK=

	*modify <tt>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).		*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>.

Mysinger: /* Running DOCK */

2009-12-05T02:56:41Z

Running DOCK

← Older revision		Revision as of 02:56, 5 December 2009
Line 1:		Line 1:
	=Running DOCK=		=Running DOCK=

	*modify <tt>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).		*modify <tt>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>.

Mysinger: /* Running DOCK */

2009-12-05T02:56:27Z

Running DOCK

← Older revision		Revision as of 02:56, 5 December 2009
Line 1:		Line 1:
	=Running DOCK=		=Running DOCK=

	*modify <tt>INDOCK</tt> and set up the desired directory structure – either manually or by running <tt>~~mksdir3~~.csh 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).		*modify <tt>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>.

Mysinger at 02:55, 5 December 2009

2009-12-05T02:55:58Z

← Older revision		Revision as of 02:55, 5 December 2009
Line 6:		Line 6:
	*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]]

Mysinger: /* Running DOCK */

2009-12-05T02:28:43Z

Running DOCK

New page

=Running DOCK=

*modify <tt>INDOCK</tt> and set up the desired directory structure – either manually or by running <tt>mksdir3.csh N1 N2 Type</tt>, where <tt>N1</tt> is the identifier of the library (1: lead-like; 2: fragment-like), <tt>N2</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 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.
*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]]