Problems: Difference between revisions
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** treatment of protonation and tautomerization is unsatisfactory | ** treatment of protonation and tautomerization is unsatisfactory | ||
** treatment of E/Z isomerism is unsatisfactory | ** treatment of E/Z isomerism is unsatisfactory | ||
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* Our Cluster has various problems | * Our Cluster has various problems | ||
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** treatment of entropy | ** treatment of entropy | ||
** treatment of desolvation | ** treatment of desolvation | ||
** treatment of induced-fit effects | |||
** ligand internal energy | ** ligand internal energy | ||
== Philosophical Problems == | == Philosophical Problems == | ||
Revision as of 19:57, 12 February 2009
Technical Problems
- ZINC has various problems
- some molecules are duplicated
- treatment of protonation and tautomerization is unsatisfactory
- treatment of E/Z isomerism is unsatisfactory
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- Our Cluster has various problems
- it is too easy to overload
- Offspring's backplane has issues
- Node O/S update - Michael has ideas
- bjork needs to be rebuilt
- garbage still needs a 4->5 upgrade
- switch in 508 not correctly negotiating with workstations
- DOCK 3.5.54 has various problems
- collisions
- out of box detection
- ligand internal energy
- DOCK 6 has various problems
Scientific Problems
- in Docking
- treatment of entropy
- treatment of desolvation
- treatment of induced-fit effects
- ligand internal energy