DUMM4 - Revision history

Therese: 13 revisions

2012-10-08T20:11:52Z

13 revisions

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Revision as of 20:11, 8 October 2012

Mysinger at 02:33, 4 November 2008

2008-11-04T02:33:47Z

← Older revision		Revision as of 02:33, 4 November 2008
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	Michael Mysinger then continued to monopolized the discussion by introducing:		Michael Mysinger then continued to monopolized the discussion by introducing:
	1)Tools to help running and analyzing dock jobs from the command line: [[MUD - Michael's Utilities for Docking]]		#Tools to help running and analyzing dock jobs from the command line: [[MUD - Michael's Utilities for Docking]]
	2)Tools to automatically generate docking flexibases and DUD style decoys: [[Automated Database Preparation]]		#Tools to automatically generate docking flexibases and DUD style decoys: [[Automated Database Preparation]]

	===Requests/Improvements===		===Requests/Improvements===

Mysinger at 02:33, 4 November 2008

2008-11-04T02:33:30Z

← Older revision		Revision as of 02:33, 4 November 2008
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	== Software updates ==		== Software updates ==

	Michael Mysinger ~~to talk~~ about improvements to DOCK:		Michael Mysinger talked about improvements to DOCK:
	1) account for solvation during minimization and in single mode		#account for solvation during minimization and during single mode
	~~2) improvements to~~ scoreopt_so		#scoreopt_so now outputs solvation energies instead of just percentage desolvations
	3) important bugfix affecting rigid molecules		#important bugfix affecting rigid molecules
			#use /raid1/soft/dock69 or later to get these changes

	Michael Mysinger to ~~talk also about~~ [[MUD - Michael's Utilities for Docking]] and [[Automated Database Preparation]].		Michael Mysinger then continued to monopolized the discussion by introducing:
			1)Tools to help running and analyzing dock jobs from the command line: [[MUD - Michael's Utilities for Docking]]
			2)Tools to automatically generate docking flexibases and DUD style decoys: [[Automated Database Preparation]]

	===Requests/Improvements===		===Requests/Improvements===
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	== Errata ==		== Errata ==
	1. The section heading "Errata" is erroneous, and should be "Erratum".		1. The section heading "Errata" is erroneous, and should be "Erratum".



	== Action Items ==		== Action Items ==

Mysinger at 20:10, 29 October 2008

2008-10-29T20:10:27Z

← Older revision		Revision as of 20:10, 29 October 2008
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	3) important bugfix affecting rigid molecules		3) important bugfix affecting rigid molecules

	Michael Mysinger to talk also about ~~MUD (Michael's utilities for DOCK), see~~ [[MUD - Michael's Utilities for Docking]].		Michael Mysinger to talk also about [[MUD - Michael's Utilities for Docking]] and [[Automated Database Preparation]].

	===Requests/Improvements===		===Requests/Improvements===

Mysinger at 20:09, 29 October 2008

2008-10-29T20:09:10Z

← Older revision		Revision as of 20:09, 29 October 2008
Line 15:		Line 15:
	3) important bugfix affecting rigid molecules		3) important bugfix affecting rigid molecules

	Michael Mysinger to talk also about MUD (Michael's utilities for DOCK), see [[MUD - Michael's Utilities for Docking].		Michael Mysinger to talk also about MUD (Michael's utilities for DOCK), see [[MUD - Michael's Utilities for Docking]].

	===Requests/Improvements===		===Requests/Improvements===

Mysinger at 20:08, 29 October 2008

2008-10-29T20:08:56Z

← Older revision		Revision as of 20:08, 29 October 2008
Line 15:		Line 15:
	3) important bugfix affecting rigid molecules		3) important bugfix affecting rigid molecules

	Michael Mysinger to talk also about MUD (Michael's utilities for DOCK).		Michael Mysinger to talk also about MUD (Michael's utilities for DOCK), see [[MUD - Michael's Utilities for Docking].

	===Requests/Improvements===		===Requests/Improvements===

Frodo at 21:25, 27 October 2008

2008-10-27T21:25:43Z

← Older revision		Revision as of 21:25, 27 October 2008
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	== Varia ==		== Varia ==


			== Errata ==
			1. The section heading "Errata" is erroneous, and should be "Erratum".

Frodo: /* Database updates */

2008-10-27T21:24:33Z

Database updates

← Older revision		Revision as of 21:24, 27 October 2008
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	''Pascal'': /raid6 is now mounted on the QB3 cluster and can be found in /bks/raid6 there.		''Pascal'': /raid6 is now mounted on the QB3 cluster and can be found in /bks/raid6 there.

			''John'': Various changes in ZINC, documented on my blog http://docking.org/. Highlights:
			* Use of Epik to compute more sensible protonation states and tautomers. First thing being fixed is those ridiculous di-amine cations. Thanks to Christian, Sarah, Michael, Pascal for enabling this.
			* Lead-like and fragment-like re-definition; new subsets in progress
			* over 1M compounds depleted (removed) from ZINC due to no longer being available.
			* correspondingly, millions of new compounds have been added to ZINC.
			* talk about the "catalog explosion problem" raised by Denise.
			* ZINC9 will appear in January. I am taking requests.
			* "dock68" version. We will release "dock69" to coincide with this meeting.

	== Varia ==		== Varia ==

Mysinger at 04:06, 25 October 2008

2008-10-25T04:06:00Z

← Older revision		Revision as of 04:06, 25 October 2008
Line 10:		Line 10:
	== Software updates ==		== Software updates ==

			Michael Mysinger to talk about improvements to DOCK:
			1) account for solvation during minimization and in single mode
			2) improvements to scoreopt_so
			3) important bugfix affecting rigid molecules

			Michael Mysinger to talk also about MUD (Michael's utilities for DOCK).

	===Requests/Improvements===		===Requests/Improvements===

Mysinger at 03:59, 25 October 2008

2008-10-25T03:59:26Z

New page

== Attendees & Time==

Date: October 29, 2008, 3:00pm -

'''Next DUM on DDD '''

== Hardware updates==

== Software updates ==

===Requests/Improvements===

== Database updates ==

''Pascal'': /raid6 is now mounted on the QB3 cluster and can be found in /bks/raid6 there.

== Varia ==

== Action Items ==

[[Category:DUMM]]

→ back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]