Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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== DOCKing == | == DOCKing == | ||
| − | + | {| cellpadding=0 width=90% | |
| − | + | |[[DOCK Tutorials]] | |
| − | + | |[[Testset Protocols]] | |
| − | + | |[[Scoring Functions]] | |
| − | + | |[[Sampling Methods]] | |
| + | |- | ||
| + | |[[ZINC Database]] | ||
| + | |[[Installing DOCK]] | ||
| + | |} | ||
== Molecular Dynamics == | == Molecular Dynamics == | ||
Revision as of 21:27, 14 October 2009
Contents
Visualization Software
Basic Linux Tools
| Unix | vi | sed - Stream Editor in Unix |
| Stupid awk tricks | Ways to remove the first line | PBS Queue |
| gdb (GNU Debugger) | Common Errors - ctrl M | C Shell Scripting |
| Unix find | Which Unix Distribution? |
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
BlueGene
| Get time estimate for free blocks | Get Job ids to use for llcancel | Get time for job completion |
| Submitting BlueGene Jobs | Compiling Applications for BG/L | Compiling Applications for BG/P |
