Rizzo Lab Information and Tutorials

DOCK

• Online Users Manual
• Tutorials
  • virtual screen, de novo design, genetic algorithm, covalent
• Benchmarking Protocols and Results
  • testset, pose reproduction, crossdocking, database enrichment SOP and other algorithm results
• Additional DOCK6 Information
  • miscellaneous information for DOCK scoring functions and experiments (some legacy)

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
• Useful Slurm Commands
• 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