Difference between revisions of "DUMM6"

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(Slides)
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== Slides ==
 
== Slides ==
  
#Philosophy
+
1. '''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
+
2. '''DOCK 3.5.54.72 improvements'''
**chem.bmp bumping instead of distmap 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
**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 (use dock.csh instead of calling directly)
**speedups (3-5x)
+
*speedups (3-5x)
  
#Deprecated keywords
+
3. '''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
  
#New keywords
+
4. '''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
+
5. '''DISI'''
**it is great
+
*it is great
 +
 
 +
 
 +
'''All of this is live since Mar 18 2010 in dock72!'''
  
 
== Hardware updates==
 
== Hardware updates==

Revision as of 17:51, 21 April 2010

Attendees & Time

Date: April 2nd, 2010. 105 pm.

Slides

1. 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. DISI

  • it is great


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

Hardware updates

Software updates

Requests/Improvements

Sandra 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

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