Rizzo Lab Information and Tutorials

DOCK

• Online Users Manual
• Tutorials
• Benchmarking
• Developer's Info
• Testset Protocols
• Parameter List/Explanations
• Scoring Functions
• Example Input Files
• DOCK Abbreviations Guide
• Advanced Dock Utilities/Information
• DOCK6 POSE Reproduction
• Virtual Screening SOP

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

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

• Analysis Tools Repository
• MATLAB
• Octave
• R - Statistical Computing
• gnuplot
• pylab

Databases

• PubChem (ligand database)
• NIST (small molecule database)
• ZINC12 Database
• ZINC15 Database
• Families in the Protein Databank
• Automated Family generation from PDB
• Drug-like organic molecules

Conversion between file types

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

Setting up accounts

• Activating your Seawulf Account
• Rotation students Wiki

AutoDock4

• AutoDock4 Pose Reproduction Tutorial
• AutoDock4 Crossdock
• AutoDock4 Benchmark Results

AutoDock Vina

• AutoDock Vina Pose Reproduction Tutorial
• AutoDock Vina Benchmark Results

Miscellaneous

• How to purchase compounds for Rizzo lab
• X-Win32
• CVS Commands
• Ethernet Cables
• Sequence alignment
• Making images for publication
• Lab-designed code and programs
• Server Administration
• Amber on Seawulf (compilation)
• Cluster compilations
• NAMD on Seawulf
• Semester Checklist
• Wiki Editing
• Other Meetings
• Seawulf Cluster Assessment
• Formatting your Thesis
• Setting up insurance through Research Foundation

Archive

• Legacy Info
• Test