Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
(→Molecular Dynamics) |
(→Molecular Dynamics) |
||
| Line 36: | Line 36: | ||
|[[NAMD tutorial]] | |[[NAMD tutorial]] | ||
|[[NAMD Amber inputs]] | |[[NAMD Amber inputs]] | ||
| + | |- | ||
|[[ptraj]] | |[[ptraj]] | ||
|} | |} | ||
Revision as of 11:11, 20 July 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 |
DOCKing
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
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 |
