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	Which Unix Distribution?	rsync
MPICH	Secure Shell (ssh)	Archiving old data
valgrind

DOCKing

DOCK Tutorials	Testset Protocols	Scoring Functions	Sampling Methods
ZINC Database	Installing DOCK	Optimize Polar Hydrogens	Virtual Screening Protocol
Sphere Generation	DOCK Compilation

Molecular Dynamics

AMBER Tutorials	AMBER TI Tutorials	AMBER tricks
NAMD tutorial	NAMD Amber inputs
per-residue energy decompositions	nonstandard residues prep
ptraj

NAMD and DOCK on BlueGene

error analysis

Blocked Standard Error of the Mean autocorrelation function

GROMACS

Compiling GROMACS on Cluster
MD Simulation: Protein in Water	MD Simulation: Protein-Ligand Complex	Membrane Protein Systems
TI: Mutating Ligand to Nothing	TI: Mutating Ligand to Ligand	Steered MD / Umbrella Sampling

Monte Carlo

• BOSS Pure Liquid Simulation Notes

Analysis Tools

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

Databases

• NCI (ligand database)
• NIST (small molecule database)
• ZINC (ligand database)
• Families in the Protein Databank
• Automated Families generation from the Protein Databank
• Drug-like organic molecules

BlueGene

Setup ssh tunnel to NYBlue fen	Get time estimate for free blocks	Get Job ids to use for llcancel
Submitting BlueGene Jobs	Compiling Applications for BG/L	LoadLeveler Chain Jobs
scp files from cluster to NYBlue	Get time for job completion

Conversion between file types

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

Setting up accounts

Getting a BNL Account

Activating your Seawulf Account

Rotation students Wiki

Setting up RSA SecureID token

Miscellaneous

X-Win32	CVS Commands	Ethernet Cables	Sequence alignment
Visiting BNL	Making images for publication	Lab-designed code and programs	Server Administration
Amber on Seawulf (compilation)	Cluster compilations	NAMD on Seawulf	Dell 5110cn Printer
Journal Articles from UCSF

Insurance

Research Foundation