DUMM6: Difference between revisions
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#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== |
Revision as of 16:19, 2 April 2010
Attendees & Time
Date: April 2nd, 2010. 105 pm.
Slides
- 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
- DOCK 3.5.54.72 improvements
- distmap bumping instead of 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 (dock.csh instead of calling directly)
- speedups (3-5x)
- 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
- write_coordinates
- standard_pdb
- focus_ratio
- New keywords
- keyword default suggested
- remove_positive_solvation no YES
- check_clashes yes YES
- DISI
- it is great
Hardware updates
Software updates
Requests/Improvements
Database updates
Varia
Errata
Action Items
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