Rizzo Lab Information and Tutorials

Visualization Software

• Chimera
• MOE
• VMD

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

• DOCK Tutorials
• Testset Protocols
• Scoring Functions
• Sampling Methods
• ZINC Database

Molecular Dynamics

AMBER Tutorials	AMBER tricks
NAMD tutorial	NAMD Amber inputs	ptraj

NAMD and DOCK on BlueGene

Monte Carlo

• BOSS Pure Liquid Simulation Notes

Analysis Tools

• MATLAB
• Octave
• R - Statistical Computing
• Xmgrace
• gnuplot

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

Conversion between file types

• Amber to pdb
• Amber to mol2 (protein)
• NAMD to mol2
• pdb to mol2

Miscellaneous

X-Win32	CVS Commands	Ethernet Cables
Getting a BNL Account	Getting a Seawulf Account	Sequence alignment
Visiting BNL	Making images for publication	Lab-designed code and programs
scp files from cluster to NYBlue	Setup ssh tunnel to NYBlue fen	Server Administration
Code Development	NAMD on Seawulf	Dell 5110cn Printer

Insurance

Research Foundation