DUMM6: Difference between revisions
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*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 | ||
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*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) | ||
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*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== |
Revision as of 16:18, 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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