DUMM6: Difference between revisions
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#DOCK 3.5.54.72 improvements | #DOCK 3.5.54.72 improvements | ||
** | **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 | ||
Revision as of 21:37, 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
- 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 (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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