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