Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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== BlueGene == | == BlueGene == | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| + | | [[Setup ssh tunnel to NYBlue fen]] | ||
| [[Get time estimate for free blocks]] | | [[Get time estimate for free blocks]] | ||
| [[Get Job ids to use for llcancel]] | | [[Get Job ids to use for llcancel]] | ||
| − | + | ||
|- | |- | ||
| [[Submitting BlueGene Jobs]] | | [[Submitting BlueGene Jobs]] | ||
| [[Compiling Applications for BG/L]] | | [[Compiling Applications for BG/L]] | ||
| [[BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)]] | | [[BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)]] | ||
| − | |- | + | |- |
| − | | | + | | [[scp files from cluster to NYBlue]] |
| + | | [[Get time for job completion]] | ||
|} | |} | ||
| Line 100: | Line 102: | ||
| [[Lab-designed code and programs]] | | [[Lab-designed code and programs]] | ||
|- | |- | ||
| − | + | ||
| − | + | ||
| [[Server Administration]] | | [[Server Administration]] | ||
|- | |- | ||
Revision as of 11:29, 8 December 2009
Contents
Visualization Software
Basic Linux Tools
DOCKing
| DOCK Tutorials | Testset Protocols | Scoring Functions | Sampling Methods |
| ZINC Database | Installing DOCK |
Molecular Dynamics
| AMBER Tutorials | AMBER tricks |
| NAMD tutorial | NAMD Amber inputs |
| ptraj |
Monte Carlo
Analysis Tools
Databases
- NCI (ligand database)
- NIST (small molecule database)
- ZINC (ligand database)
- Families in the Protein Databank
- Drug-like organic molecules
