DUMM6 - Revision history

Therese: 13 revisions

2012-10-08T20:11:52Z

13 revisions

New page

== Attendees & Time==

Sarah, Michael M, Ryan, Magdalena, Peter, Kong, Jens, Dahlia, John

Date: April 2nd, 2010. 1:05 pm.

== Slides ==

1. '''[http://www.urbandictionary.com/define.php?term=philosophy Philosophy]'''
*deleted unused things
*cleaned up code
*streamlined call graph
*single mode gone (use version 3.5.54.70)
*contact scoring gone
*precalculate various grid terms

2. '''[[DOCK 3.5.54]].72 improvements'''
*chem.bmp bumping instead of distmap contact bumping
*new hierarchy code (should eliminate some broken)
*no more out of bounds molecules
*no more clashing molecules
*deprecated unused keywords (more later)
*vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
*64bit/32bit builds (use dock.csh instead of calling directly)
*speedups (3-5x)

3. '''Deprecated keywords'''
*write_coordinates
*standard_pdb
*focus_ratio
*normalize_save
*restart_interval
*mirror_ligands
*scoring_option
*mode
*ligand_type
*restart
*output_hydrogens
*recombine_fragments
*interpolate
*ligand_sphere_file

4. '''New keywords'''
*keyword default suggested
*remove_positive_solvation no YES
*check_clashes yes YES

5. '''[[Main_Page|DISI]]'''
*it is great

'''All of this is live since Mar 18 2010 in dock72!'''

== Hardware updates==

== Software updates ==

== Requests/Improvements ==

Sarah raised the issue of the flexible protein code of Niu Huang:

* Is it compatible with the current improvements? <math>\rightarrow</math> probably not.
* Is anybody using it?
* Would it be worth it to update and include it?
* Can it be used in an automatic fashion, e.g. for [[DOCK Blaster]]?
* How can we predict water positions and usefulness (maybe initial water placement with [[PLOP]])?

<math>\Rightarrow</math> who will be doing all of this?

== Database updates ==

== Varia ==

== Errata ==

== Action Items ==

[[Category:DUMM]]

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

Rgc: /* Slides */ removing duplicates

2010-04-02T23:12:45Z

Slides: removing duplicates

← Older revision		Revision as of 23:12, 2 April 2010
Line 38:		Line 38:
	**interpolate		**interpolate
	**ligand_sphere_file		**ligand_sphere_file
	**write_coordinates
	**standard_pdb
	**focus_ratio

	#New keywords		#New keywords

Rgc: /* Slides */ fixing error

2010-04-02T21:37:21Z

Slides: fixing error

← Older revision		Revision as of 21:37, 2 April 2010
Line 14:		Line 14:

	#DOCK 3.5.54.72 improvements		#DOCK 3.5.54.72 improvements
	**~~distmap~~ bumping instead of contact bumping		**chem.bmp bumping instead of distmap contact bumping
	**new hierarchy code (should eliminate some broken)		**new hierarchy code (should eliminate some broken)
	**no more out of bounds molecules		**no more out of bounds molecules

Rgc: formatting

2010-04-02T16:19:31Z

formatting

← Older revision		Revision as of 16:19, 2 April 2010
Line 6:		Line 6:

	#Philosophy		#Philosophy
	*deleted unused things		**deleted unused things
	*cleaned up code		**cleaned up code
	*streamlined call graph		**streamlined call graph
	**single mode gone (use version 3.5.54.70)		***single mode gone (use version 3.5.54.70)
	**contact scoring gone		***contact scoring gone
	**precalculate various grid terms		***precalculate various grid terms

	#DOCK 3.5.54.72 improvements		#DOCK 3.5.54.72 improvements
	*distmap bumping instead of contact bumping		**distmap bumping instead of contact bumping
	*new hierarchy code (should eliminate some broken)		**new hierarchy code (should eliminate some broken)
	*no more out of bounds molecules		**no more out of bounds molecules
	*no more clashing molecules		**no more clashing molecules
	*deprecated unused keywords (more later)		**deprecated unused keywords (more later)
	*vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)		**vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
	*64bit/32bit builds (dock.csh instead of calling directly)		**64bit/32bit builds (dock.csh instead of calling directly)
	*speedups (3-5x)		**speedups (3-5x)

	#Deprecated keywords		#Deprecated keywords
	*write_coordinates		**write_coordinates
	*standard_pdb		**standard_pdb
	*focus_ratio		**focus_ratio
	*normalize_save		**normalize_save
	*restart_interval		**restart_interval
	*mirror_ligands		**mirror_ligands
	*scoring_option		**scoring_option
	*mode		**mode
	*ligand_type		**ligand_type
	*restart		**restart
	*output_hydrogens		**output_hydrogens
	*recombine_fragments		**recombine_fragments
	*interpolate		**interpolate
	*ligand_sphere_file		**ligand_sphere_file
	*write_coordinates		**write_coordinates
	*standard_pdb		**standard_pdb
	*focus_ratio		**focus_ratio

	#New keywords		#New keywords
	*keyword default suggested		**keyword default suggested
	*remove_positive_solvation no YES		**remove_positive_solvation no YES
	*check_clashes yes YES		**check_clashes yes YES

	#DISI		#DISI
	*it is great		**it is great

	== Hardware updates==		== Hardware updates==

Rgc: update

2010-04-02T16:18:40Z

update

← Older revision		Revision as of 16:18, 2 April 2010
Line 9:		Line 9:
	*cleaned up code		*cleaned up code
	*streamlined call graph		*streamlined call graph
	*single mode gone (use version 3.5.54.70)		**single mode gone (use version 3.5.54.70)
	*contact scoring gone		**contact scoring gone
			**precalculate various grid terms

	#DOCK 3.5.54.72 improvements		#DOCK 3.5.54.72 improvements
Line 17:		Line 18:
	*no more out of bounds molecules		*no more out of bounds molecules
	*no more clashing molecules		*no more clashing molecules
	*deprecated unused keywords		*deprecated unused keywords (more later)
			*vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
	*64bit/32bit builds (dock.csh instead of calling directly)		*64bit/32bit builds (dock.csh instead of calling directly)
	*speedups (3-5x)		*speedups (3-5x)
Line 44:		Line 46:
	*remove_positive_solvation no YES		*remove_positive_solvation no YES
	*check_clashes yes YES		*check_clashes yes YES

			#DISI
			*it is great

	== Hardware updates==		== Hardware updates==

Rgc: adding slides

2010-04-02T00:05:27Z

adding slides

@@ Line 1: / Line 1: @@
 == Attendees & Time==
-Date: ???, 2010, ? - ?
+Date: April 2nd, 2010. 105 pm.
 == Hardware updates==

Rgc: formatting

2010-03-19T22:52:41Z

formatting

← Older revision		Revision as of 22:52, 19 March 2010
Line 8:		Line 8:
	== Software updates ==		== Software updates ==

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

Rgc: making a page for the next as yet unscheduled DUMM meeting

2010-03-19T22:49:48Z

making a page for the next as yet unscheduled DUMM meeting

New page

== Attendees & Time==

Date: ???, 2010, ? - ?

== Hardware updates==

== Software updates ==

===Requests/Improvements===

== Database updates ==

== Varia ==

== Errata ==

== Action Items ==

[[Category:DUMM]]

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