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
• Formatting your Thesis
• Setting up insurance through Research Foundation

Archive

• Legacy Info