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)

DOCKing

DOCK Tutorials	Testset Protocols	Scoring Functions	Sampling Methods
ZINC Database	Installing DOCK	Optimize Polar Hydrogens	Virtual Screening Protocol} Molecular Dynamics AMBER Tutorials AMBER TI 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 pylab Databases NCI (ligand database) NIST (small molecule database) ZINC (ligand database) Families in 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 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) NAMD on Seawulf Dell 5110cn Printer Insurance Research Foundation