Rizzo Lab Information and Tutorials

Visualization Software

• Chimera
• MOE
• VMD

Basic Linux Tools

• Unix
• vi
• sed - Stream Editor in Unix
• Slick 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
• Ghostscript

Docking

DOCK Tutorials	Covalent DOCK	Testset Protocols	Scoring Functions	Sampling Methods	3D Analog Library Generation Using Pubchem and Zinc
ZINC12 Database	ZINC15 Database	Installing DOCK	Optimize Polar Hydrogens	Virtual Screening Protocol	Footprint Plot Visualization
Sphere Generation	DOCK Compilation	Virtual Screening Protocol on BlueGene (IGF-IR system)	DOCK Benchmarking	Release

De novo Design using DOCK

• De Novo Design (DOCK_DN)
• Small Molecule Evolution (DOCK_GA)

Molecular Dynamics

AMBER Tutorials	AMBER TI Tutorials	AMBER Lipid Tutorials	AMBER tricks
NAMD tutorial	NAMD Amber inputs
per-residue energy decompositions	nonstandard residues prep
ptraj
Blocked Standard Error of the Mean

GROMACS

• Compiling GROMACS on Cluster
• MD Simulation: Protein in Water

Monte Carlo

• BOSS Pure Liquid Simulation Notes

Analysis Tools

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

Databases

• PubChem (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
Semester Checklist	Wiki Editing
Stony Brook Joint Group Meetings in Computational Structural Biology	Other Meetings	Seawulf Cluster Assessment

Formating Word Documents

Formating your Thesis

Insurance

Research Foundation

Archive

Legacy Info